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Naidoo Y, Pierneef RE, Cowan DA, Valverde A. Characterization of the soil resistome and mobilome in Namib Desert soils. Int Microbiol 2024; 27:967-975. [PMID: 37968548 PMCID: PMC11300574 DOI: 10.1007/s10123-023-00454-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 11/17/2023]
Abstract
The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics.
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Affiliation(s)
- Yashini Naidoo
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa.
| | - Rian E Pierneef
- Biotechnology Platform, Agricultural Research Council, Soutpan Road, Onderstepoort Campus, Pretoria, 0110, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
| | - Angel Valverde
- IRNASA-CSIC, Cordel de Merinas, 37008, Salamanca, Spain.
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2
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Bosch J, Lebre PH, Marais E, Maggs‐Kölling G, Cowan DA. Kinetics and pathways of sub-lithic microbial community (hypolithon) development. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13290. [PMID: 38923208 PMCID: PMC11194044 DOI: 10.1111/1758-2229.13290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/03/2024] [Indexed: 06/28/2024]
Abstract
Type I hypolithons are microbial communities dominated by Cyanobacteria. They adhere to the underside of semi-translucent rocks in desert pavements, providing them with a refuge from the harsh abiotic stresses found on the desert soil surface. Despite their crucial role in soil nutrient cycling, our understanding of their growth rates and community development pathways remains limited. This study aimed to quantify the dynamics of hypolithon formation in the pavements of the Namib Desert. We established replicate arrays of sterile rock tiles with varying light transmission in two areas of the Namib Desert, each with different annual precipitation regimes. These were sampled annually over 7 years, and the samples were analysed using eDNA extraction and 16S rRNA gene amplicon sequencing. Our findings revealed that in the zone with higher precipitation, hypolithon formation became evident in semi-translucent rocks 3 years after the arrays were set up. This coincided with a Cyanobacterial 'bloom' in the adherent microbial community in the third year. In contrast, no visible hypolithon formation was observed at the array set up in the hyper-arid zone. This study provides the first quantitative evidence of the kinetics of hypolithon development in hot desert environments, suggesting that development rates are strongly influenced by precipitation regimes.
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Affiliation(s)
- Jason Bosch
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoriaSouth Africa
- Institute of Microbiology of the Czech Academy of SciencesCzech Academy of SciencesPrahaCzech Republic
| | - Pedro H. Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoriaSouth Africa
| | | | | | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoriaSouth Africa
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3
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Melo de Queiroz T, Valdes TA, Leitão A, Porto ALM. Bio-oxidation of progesterone by Penicillium oxalicum CBMAI 1185 and evaluation of the cytotoxic activity. Steroids 2024; 205:109392. [PMID: 38452910 DOI: 10.1016/j.steroids.2024.109392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
We report the biotransformation of progesterone 1 by whole cells of Brazilian marine-derived fungi. A preliminary screening with 12 fungi revealed that the strains Penicillium oxalicum CBMAI 1996, Mucor racemous CBMAI 847, Cladosporium sp. CBMAI 1237, Penicillium oxalicum CBMAI 1185 and Aspergillus sydowii CBMAI 935 were efficient in the biotransformation of progesterone 1 in the first days of the reaction, with conversion values ranging from 75 % to 99 %. The fungus P. oxalicum CBMAI 1185 was employed in the reactions in quintuplicate to purify and characterize the main biotransformation products of progesterone 1. The compounds testololactone 1a, 12β-hydroxyandrostenedione 1b and 1β-hydroxyandrostenedione 1c were isolated and characterized by NMR, MS, [α]D and MP. In addition, the chromatographic yield of compound 1a was determined by HPLC-PDA in the screening experiments. In this study, we show a biotransformation pathway of progesterone 1, suggesting the presence of several enzymes such as Baeyer-Villiger monooxygenases, dehydrogenases and cytochrome P450 monooxygenases in the fungus P. oxalicum CBMAI 1185. In summary, the results obtained in this study contribute to the synthetic area and have environmental importance, since the marine-derived fungi can be employed in the biodegradation of steroids present in wastewater and the environment. The cytotoxic results demonstrate that the biodegradation products were inactive against the cell lines, in contrast to progesterone.
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Affiliation(s)
- Thayane Melo de Queiroz
- Laboratório de Química Orgânica e Biocatálise, Instituto de Química de São Carlos, Universidade de São Paulo, Av. João Dagnone, 1100, Química Ambiental "Edifício Prof. Douglas Wagner Franco", Santa Angelina, 13563-120 São Carlos, SP, Brazil
| | - Talita A Valdes
- Medicinal & Biological Chemistry Group, Instituto de Química de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-Carlense, 400, 13566-590, São Carlos, SP, Brazil
| | - Andrei Leitão
- Medicinal & Biological Chemistry Group, Instituto de Química de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-Carlense, 400, 13566-590, São Carlos, SP, Brazil
| | - André L M Porto
- Laboratório de Química Orgânica e Biocatálise, Instituto de Química de São Carlos, Universidade de São Paulo, Av. João Dagnone, 1100, Química Ambiental "Edifício Prof. Douglas Wagner Franco", Santa Angelina, 13563-120 São Carlos, SP, Brazil.
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Li X, Li Q, Duan Y, Sun H, Chu H, Jia S, Chen H, Tang W. Soil fungal communities varied across aspects of restored grassland in former mining areas of the Qinghai-Tibet Plateau. PLoS One 2024; 19:e0295019. [PMID: 38530822 DOI: 10.1371/journal.pone.0295019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 11/14/2023] [Indexed: 03/28/2024] Open
Abstract
To determine whether different aspects lead to a heterogeneous distribution of soil fungi, we investigated artificially established alpine grasslands in the Muli mining area in the Qinghai-Tibet Plateau. Employing high-throughput sequencing techniques, we analyzed the composition, diversity, and function of soil fungal communities across various aspects (flat, East-facing, South-facing, West-facing, North-facing). We also examined their relationships with environmental factors. Soil fungal communities of restored alpine grasslands differed significantly across aspects in terms of the dominant phyla, classes and species level. Compared with No aspect, the Shannon index of fungi respectively decreased by 2.99%, 19.32%, 19.37% and 10.56% for East aspect, South aspect, West aspect and North aspect, respectively, and the Chao1 index of fungi respectively decreased by-2.44%, 35.50%, 42.15% and 3.21%, respectively. A total of 22 different types of fungi were identified in the study area. Predictive analysis, based on PICRUSt2, indicated that the primary functions of the fungal communities across different aspects were aerobic respiration I (cytochrome c) and aerobic respiration II (cytochrome c). Among the environmental variables, total phosphorus (P) and total nitrogen (N) were the principal factors influencing the fungal community composition.In conclusion, aspect plays a significant role in shaping the composition of fungal communities and also affects their overall diversity.
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Affiliation(s)
- Xiaoqing Li
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Qiang Li
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Yinzhu Duan
- Qinghai Province Grassland Improvement Experiment Station, Xining, China
| | - Haiqun Sun
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Hui Chu
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Shunbin Jia
- Qinghai Province Grassland Technology and Extension Station, Xining, China
| | - Hongjie Chen
- Tongyu County Animal Quarantine Station, Baicheng, China
| | - Wenxi Tang
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
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Kashani M, Engle MA, Kent DB, Gregston T, Cozzarelli IM, Mumford AC, Varonka MS, Harris CR, Akob DM. Illegal dumping of oil and gas wastewater alters arid soil microbial communities. Appl Environ Microbiol 2024; 90:e0149023. [PMID: 38294246 PMCID: PMC10880632 DOI: 10.1128/aem.01490-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/27/2023] [Indexed: 02/01/2024] Open
Abstract
The Permian Basin, underlying southeast New Mexico and west Texas, is one of the most productive oil and gas (OG) provinces in the United States. Oil and gas production yields large volumes of wastewater with complex chemistries, and the environmental health risks posed by these OG wastewaters on sensitive desert ecosystems are poorly understood. Starting in November 2017, 39 illegal dumps, as defined by federal and state regulations, of OG wastewater were identified in southeastern New Mexico, releasing ~600,000 L of fluid onto dryland soils. To evaluate the impacts of these releases, we analyzed changes in soil geochemistry and microbial community composition by comparing soils from within OG wastewater dump-affected samples to unaffected zones. We observed significant changes in soil geochemistry for all dump-affected compared with control samples, reflecting the residual salts and hydrocarbons from the OG-wastewater release (e.g., enriched in sodium, chloride, and bromide). Microbial community structure significantly (P < 0.01) differed between dump and control zones, with soils from dump areas having significantly (P < 0.01) lower alpha diversity and differences in phylogenetic composition. Dump-affected soil samples showed an increase in halophilic and halotolerant taxa, including members of the Marinobacteraceae, Halomonadaceae, and Halobacteroidaceae, suggesting that the high salinity of the dumped OG wastewater was exerting a strong selective pressure on microbial community structure. Taxa with high similarity to known hydrocarbon-degrading organisms were also detected in the dump-affected soil samples. Overall, this study demonstrates the potential for OG wastewater exposure to change the geochemistry and microbial community dynamics of arid soils.IMPORTANCEThe long-term environmental health impacts resulting from releases of oil and gas (OG) wastewater, typically brines with varying compositions of ions, hydrocarbons, and other constituents, are understudied. This is especially true for sensitive desert ecosystems, where soil microbes are key primary producers and drivers of nutrient cycling. We found that releases of OG wastewater can lead to shifts in microbial community composition and function toward salt- and hydrocarbon-tolerant taxa that are not typically found in desert soils, thus altering the impacted dryland soil ecosystem. Loss of key microbial taxa, such as those that catalyze organic carbon cycling, increase arid soil fertility, promote plant health, and affect soil moisture retention, could result in cascading effects across the sensitive desert ecosystem. By characterizing environmental changes due to releases of OG wastewater to soils overlying the Permian Basin, we gain further insights into how OG wastewater may alter dryland soil microbial functions and ecosystems.
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Affiliation(s)
- Mitra Kashani
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
| | - Mark A Engle
- Department of Earth, Environmental and Resource Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Douglas B Kent
- U.S. Geological Survey, Earth Systems Processes Division, Menlo Park, California, USA
| | | | - Isabelle M Cozzarelli
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
| | - Adam C Mumford
- U.S. Geological Survey, Maryland-Delaware-D.C. Water Science Center, Baltimore, Maryland, USA
| | - Matthew S Varonka
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
| | - Cassandra R Harris
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
| | - Denise M Akob
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
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Huang Z, Yu X, Liu Q, Maki T, Alam K, Wang Y, Xue F, Tang S, Du P, Dong Q, Wang D, Huang J. Bioaerosols in the atmosphere: A comprehensive review on detection methods, concentration and influencing factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168818. [PMID: 38036132 DOI: 10.1016/j.scitotenv.2023.168818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/02/2023]
Abstract
In the past few decades, especially since the outbreak of the coronavirus disease (COVID-19), the effects of atmospheric bioaerosols on human health, the environment, and climate have received great attention. To evaluate the impacts of bioaerosols quantitatively, it is crucial to determine the types of bioaerosols in the atmosphere and their spatial-temporal distribution. We provide a concise summary of the online and offline observation strategies employed by the global research community to sample and analyze atmospheric bioaerosols. In addition, the quantitative distribution of bioaerosols is described by considering the atmospheric bioaerosols concentrations at various time scales (daily and seasonal changes, for example), under various weather, and different underlying surfaces. Finally, a comprehensive summary of the reasons for the spatiotemporal distribution of bioaerosols is discussed, including differences in emission sources, the impact process of meteorological factors and environmental factors. This review of information on the latest research progress contributes to the emergence of further observation strategies that determine the quantitative dynamics of public health and ecological effects of bioaerosols.
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Affiliation(s)
- Zhongwei Huang
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China; Collaborative Innovation Center for Western Ecological Safety, Lanzhou University, Lanzhou 730000, China
| | - Xinrong Yu
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Qiantao Liu
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Teruya Maki
- Department of Life Science, Faculty of Science and Engineering, Kindai University, Higashiosaka, Osaka, Japan
| | - Khan Alam
- Department of Physics, University of Peshawar, Peshawar 25120, Pakistan
| | - Yongkai Wang
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Fanli Xue
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Shihan Tang
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Pengyue Du
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Qing Dong
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Danfeng Wang
- Collaborative Innovation Center for Western Ecological Safety, Lanzhou University, Lanzhou 730000, China
| | - Jianping Huang
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China; Collaborative Innovation Center for Western Ecological Safety, Lanzhou University, Lanzhou 730000, China.
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Savaglia V, Lambrechts S, Tytgat B, Vanhellemont Q, Elster J, Willems A, Wilmotte A, Verleyen E, Vyverman W. Geology defines microbiome structure and composition in nunataks and valleys of the Sør Rondane Mountains, East Antarctica. Front Microbiol 2024; 15:1316633. [PMID: 38380088 PMCID: PMC10877063 DOI: 10.3389/fmicb.2024.1316633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/09/2024] [Indexed: 02/22/2024] Open
Abstract
Understanding the relation between terrestrial microorganisms and edaphic factors in the Antarctic can provide insights into their potential response to environmental changes. Here we examined the composition of bacterial and micro-eukaryotic communities using amplicon sequencing of rRNA genes in 105 soil samples from the Sør Rondane Mountains (East Antarctica), differing in bedrock or substrate type and associated physicochemical conditions. Although the two most widespread taxa (Acidobacteriota and Chlorophyta) were relatively abundant in each sample, multivariate analysis and co-occurrence networks revealed pronounced differences in community structure depending on substrate type. In moraine substrates, Actinomycetota and Cercozoa were the most abundant bacterial and eukaryotic phyla, whereas on gneiss, granite and marble substrates, Cyanobacteriota and Metazoa were the dominant bacterial and eukaryotic taxa. However, at lower taxonomic level, a distinct differentiation was observed within the Cyanobacteriota phylum depending on substrate type, with granite being dominated by the Nostocaceae family and marble by the Chroococcidiopsaceae family. Surprisingly, metazoans were relatively abundant according to the 18S rRNA dataset, even in samples from the most arid sites, such as moraines in Austkampane and Widerøefjellet ("Dry Valley"). Overall, our study shows that different substrate types support distinct microbial communities, and that mineral soil diversity is a major determinant of terrestrial microbial diversity in inland Antarctic nunataks and valleys.
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Affiliation(s)
- Valentina Savaglia
- InBioS Research Unit, Department of Life Sciences, University of Liège, Liège, Belgium
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Sam Lambrechts
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Bjorn Tytgat
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | | | - Josef Elster
- Faculty of Science, Centre for Polar Ecology, University of South Bohemia České Budějovice and Institute of Botany, Třeboň, Czechia
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Annick Wilmotte
- InBioS Research Unit, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Elie Verleyen
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
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Coleine C, Delgado-Baquerizo M, DiRuggiero J, Guirado E, Harfouche AL, Perez-Fernandez C, Singh BK, Selbmann L, Egidi E. Dryland microbiomes reveal community adaptations to desertification and climate change. THE ISME JOURNAL 2024; 18:wrae056. [PMID: 38552152 PMCID: PMC11031246 DOI: 10.1093/ismejo/wrae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/21/2024]
Abstract
Drylands account for 45% of the Earth's land area, supporting ~40% of the global population. These regions support some of the most extreme environments on Earth, characterized by extreme temperatures, low and variable rainfall, and low soil fertility. In these biomes, microorganisms provide vital ecosystem services and have evolved distinctive adaptation strategies to endure and flourish in the extreme. However, dryland microbiomes and the ecosystem services they provide are under threat due to intensifying desertification and climate change. In this review, we provide a synthesis of our current understanding of microbial life in drylands, emphasizing the remarkable diversity and adaptations of these communities. We then discuss anthropogenic threats, including the influence of climate change on dryland microbiomes and outline current knowledge gaps. Finally, we propose research priorities to address those gaps and safeguard the sustainability of these fragile biomes.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, E-41012, Spain
| | - Jocelyne DiRuggiero
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, United States
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Emilio Guirado
- Multidisciplinary Institute for Environment Studies “Ramón Margalef”, Universidad de Alicante, Alicante E-03071, Spain
| | - Antoine L Harfouche
- Department for Innovation in Biological, Agro-Food and Forest systems, University of Tuscia, Viterbo 01100, Italy
| | | | - Brajesh K Singh
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith 2750, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith 2750, Australia
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy
- Mycological Section, Italian Antarctic National Museum (MNA), Genoa 16128, Italy
| | - Eleonora Egidi
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith 2750, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith 2750, Australia
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9
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Santander C, González F, Pérez U, Ruiz A, Aroca R, Santos C, Cornejo P, Vidal G. Enhancing Water Status and Nutrient Uptake in Drought-Stressed Lettuce Plants ( Lactuca sativa L.) via Inoculation with Different Bacillus spp. Isolated from the Atacama Desert. PLANTS (BASEL, SWITZERLAND) 2024; 13:158. [PMID: 38256712 PMCID: PMC10818642 DOI: 10.3390/plants13020158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/26/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024]
Abstract
Drought is a major challenge for agriculture worldwide, being one of the main causes of losses in plant production. Various studies reported that some soil's bacteria can improve plant tolerance to environmental stresses by the enhancement of water and nutrient uptake by plants. The Atacama Desert in Chile, the driest place on earth, harbors a largely unexplored microbial richness. This study aimed to evaluate the ability of various Bacillus sp. from the hyper arid Atacama Desert in the improvement in tolerance to drought stress in lettuce (Lactuca sativa L. var. capitata, cv. "Super Milanesa") plants. Seven strains of Bacillus spp. were isolated from the rhizosphere of the Chilean endemic plants Metharme lanata and Nolana jaffuelii, and then identified using the 16s rRNA gene. Indole acetic acid (IAA) production, phosphate solubilization, nitrogen fixation, and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity were assessed. Lettuce plants were inoculated with Bacillus spp. strains and subjected to two different irrigation conditions (95% and 45% of field capacity) and their biomass, net photosynthesis, relative water content, photosynthetic pigments, nitrogen and phosphorus uptake, oxidative damage, proline production, and phenolic compounds were evaluated. The results indicated that plants inoculated with B. atrophaeus, B. ginsengihumi, and B. tequilensis demonstrated the highest growth under drought conditions compared to non-inoculated plants. Treatments increased biomass production and were strongly associated with enhanced N-uptake, water status, chlorophyll content, and photosynthetic activity. Our results show that specific Bacillus species from the Atacama Desert enhance drought stress tolerance in lettuce plants by promoting several beneficial plant traits that facilitate water absorption and nutrient uptake, which support the use of this unexplored and unexploited natural resource as potent bioinoculants to improve plant production under increasing drought conditions.
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Affiliation(s)
- Christian Santander
- Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco 4811230, Chile; (C.S.); (F.G.); (U.P.); (A.R.); (C.S.)
- Grupo de Ingeniería Ambiental y Biotecnología, Facultad de Ciencias Ambientales y Centro EULA-Chile, Universidad de Concepción, Concepción 4070411, Chile
| | - Felipe González
- Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco 4811230, Chile; (C.S.); (F.G.); (U.P.); (A.R.); (C.S.)
- Programa de Doctorado en Ciencias Mención Biología Celular y Molecular Aplicada, Universidad de La Frontera, Temuco 4811230, Chile
| | - Urley Pérez
- Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco 4811230, Chile; (C.S.); (F.G.); (U.P.); (A.R.); (C.S.)
| | - Antonieta Ruiz
- Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco 4811230, Chile; (C.S.); (F.G.); (U.P.); (A.R.); (C.S.)
| | - Ricardo Aroca
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, CSIC, Profesor Albareda 1, 18008 Granada, Spain;
| | - Cledir Santos
- Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco 4811230, Chile; (C.S.); (F.G.); (U.P.); (A.R.); (C.S.)
| | - Pablo Cornejo
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Quillota 2260000, Chile
- Centro Regional de Investigación e Innovación para la Sostenibilidad de la Agricultura y los Territorios Rurales, CERES, La Palma, Quillota 2260000, Chile
| | - Gladys Vidal
- Grupo de Ingeniería Ambiental y Biotecnología, Facultad de Ciencias Ambientales y Centro EULA-Chile, Universidad de Concepción, Concepción 4070411, Chile
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Boivin S, Bourceret A, Maurice K, Laurent-Webb L, Figura T, Bourillon J, Nespoulous J, Domergue O, Chaintreuil C, Boukcim H, Selosse MA, Fiema Z, Botte E, Nehme L, Ducousso M. Revealing human impact on natural ecosystems through soil bacterial DNA sampled from an archaeological site. Environ Microbiol 2024; 26:e16546. [PMID: 38086774 DOI: 10.1111/1462-2920.16546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 11/17/2023] [Indexed: 01/30/2024]
Abstract
Human activities have affected the surrounding natural ecosystems, including belowground microorganisms, for millennia. Their short- and medium-term effects on the diversity and the composition of soil microbial communities are well-documented, but their lasting effects remain unknown. When unoccupied for centuries, archaeological sites are appropriate for studying the long-term effects of past human occupancy on natural ecosystems, including the soil compartment. In this work, the soil chemical and bacterial compositions were compared between the Roman fort of Hegra (Saudi Arabia) abandoned for 1500 years, and a preserved area located at 120 m of the southern wall of the Roman fort where no human occupancy was detected. We show that the four centuries of human occupancy have deeply and lastingly modified both the soil chemical and bacterial compositions inside the Roman fort. We also highlight different bacterial putative functions between the two areas, notably associated with human occupancy. Finally, this work shows that the use of soils from archaeological sites causes little disruption and can bring relevant information, at a large scale, during the initial surveys of archaeological sites.
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Affiliation(s)
- Stéphane Boivin
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), CIRAD, IRD, INRAE, University of Montpellier, Montpellier SupAgro, Montpellier, France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
- Valorhiz, Montferrier sur Lez, France
| | - Amélia Bourceret
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Kenji Maurice
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), CIRAD, IRD, INRAE, University of Montpellier, Montpellier SupAgro, Montpellier, France
| | - Liam Laurent-Webb
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Tomáš Figura
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
- Faculty of Science, Department of Experimental Plant Biology, Charles University, Prague, Czech Republic
| | - Julie Bourillon
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), CIRAD, IRD, INRAE, University of Montpellier, Montpellier SupAgro, Montpellier, France
| | | | - Odile Domergue
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), CIRAD, IRD, INRAE, University of Montpellier, Montpellier SupAgro, Montpellier, France
| | - Clémence Chaintreuil
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), CIRAD, IRD, INRAE, University of Montpellier, Montpellier SupAgro, Montpellier, France
| | | | - Marc-André Selosse
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
- Institut Universitaire de France, Paris, France
- Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, Gdańsk, Poland
| | - Zbigniew Fiema
- Department of Culture, Faculty of Art, University of Helsinki, Helsinki, Finland
| | - Emmanuel Botte
- Centre Camille Julian, CNRS, Université Aix-Marseille, Aix en Provence, France
| | - Laila Nehme
- CNRS, Orient et Méditerranée: Textes, Archéologie, Histoire, Paris, France
| | - Marc Ducousso
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), CIRAD, IRD, INRAE, University of Montpellier, Montpellier SupAgro, Montpellier, France
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11
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Martínez-Alvarez L, Ramond JB, Vikram S, León-Sobrino C, Maggs-Kölling G, Cowan DA. With a pinch of salt: metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities. Appl Environ Microbiol 2023; 89:e0062923. [PMID: 37971255 PMCID: PMC10734447 DOI: 10.1128/aem.00629-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/24/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE The hyperarid Namib Desert is one of the oldest deserts on Earth. It contains multiple clusters of playas which are saline-rich springs surrounded by halite evaporites. Playas are of great ecological importance, and their indigenous (poly)extremophilic microorganisms are potentially involved in the precipitation of minerals such as carbonates and sulfates and have been of great biotechnological importance. While there has been a considerable amount of microbial ecology research performed on various Namib Desert edaphic microbiomes, little is known about the microbial communities inhabiting its multiple playas. In this work, we provide a comprehensive taxonomic and functional potential characterization of the microbial, including viral, communities of sediment mats and halites from two distant salt pans of the Namib Desert, contributing toward a better understanding of the ecology of this biome.
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Affiliation(s)
- Laura Martínez-Alvarez
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
| | - Jean-Baptiste Ramond
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
- Extreme Ecosystem Microbiomics & Ecogenomics (E²ME) Lab., Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Surendra Vikram
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
| | - Carlos León-Sobrino
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
| | | | - Don A. Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics (CMEG), University of Pretoria, Pretoria, South Africa
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12
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Hakobyan A, Velte S, Sickel W, Quandt D, Stoll A, Knief C. Tillandsia landbeckii phyllosphere and laimosphere as refugia for bacterial life in a hyperarid desert environment. MICROBIOME 2023; 11:246. [PMID: 37936139 PMCID: PMC10631034 DOI: 10.1186/s40168-023-01684-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/28/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND The lack of water is a major constraint for microbial life in hyperarid deserts. Consequently, the abundance and diversity of microorganisms in common habitats such as soil are strongly reduced, and colonization occurs primarily by specifically adapted microorganisms that thrive in particular refugia to escape the harsh conditions that prevail in these deserts. We suggest that plants provide another refugium for microbial life in hyperarid deserts. We studied the bacterial colonization of Tillandsia landbeckii (Bromeliaceae) plants, which occur in the hyperarid regions of the Atacama Desert in Chile, one of the driest and oldest deserts on Earth. RESULTS We detected clear differences between the bacterial communities being plant associated to those of the bare soil surface (PERMANOVA, R2 = 0.187, p = 0.001), indicating that Tillandsia plants host a specific bacterial community, not only dust-deposited cells. Moreover, the bacterial communities in the phyllosphere were distinct from those in the laimosphere, i.e., on buried shoots (R2 = 0.108, p = 0.001), indicating further habitat differentiation within plant individuals. The bacterial taxa detected in the phyllosphere are partly well-known phyllosphere colonizers, but in addition, some rather unusual taxa (subgroup2 Acidobacteriae, Acidiphilum) and insect endosymbionts (Wolbachia, "Candidatus Uzinura") were found. The laimosphere hosted phyllosphere-associated as well as soil-derived taxa. The phyllosphere bacterial communities showed biogeographic patterns across the desert (R2 = 0.331, p = 0.001). These patterns were different and even more pronounced in the laimosphere (R2 = 0.467, p = 0.001), indicating that different factors determine community assembly in the two plant compartments. Furthermore, the phyllosphere microbiota underwent temporal changes (R2 = 0.064, p = 0.001). CONCLUSIONS Our data demonstrate that T. landbeckii plants host specific bacterial communities in the phyllosphere as well as in the laimosphere. Therewith, these plants provide compartment-specific refugia for microbial life in hyperarid desert environments. The bacterial communities show biogeographic patterns and temporal variation, as known from other plant microbiomes, demonstrating environmental responsiveness and suggesting that bacteria inhabit these plants as viable microorganisms. Video Abstract.
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Affiliation(s)
- Anna Hakobyan
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
| | - Stefanie Velte
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
| | - Wiebke Sickel
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
- Institute of Biodiversity, Johann Heinrich Von Thünen Institute, Brunswick, Germany
| | - Dietmar Quandt
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany
| | - Alexandra Stoll
- Centro de Estudios Avanzados en Zonas Áridas Ceaza, La Serena, Chile
- Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de La Serena, La Serena, Chile
| | - Claudia Knief
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany.
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13
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Antonaru LA, Selinger VM, Jung P, Di Stefano G, Sanderson ND, Barker L, Wilson DJ, Büdel B, Canniffe DP, Billi D, Nürnberg DJ. Common loss of far-red light photoacclimation in cyanobacteria from hot and cold deserts: a case study in the Chroococcidiopsidales. ISME COMMUNICATIONS 2023; 3:113. [PMID: 37857858 PMCID: PMC10587186 DOI: 10.1038/s43705-023-00319-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/29/2023] [Accepted: 10/05/2023] [Indexed: 10/21/2023]
Abstract
Deserts represent an extreme challenge for photosynthetic life. Despite their aridity, they are often inhabited by diverse microscopic communities of cyanobacteria. These organisms are commonly found in lithic habitats, where they are partially sheltered from extremes of temperature and UV radiation. However, living under the rock surface imposes additional constraints, such as limited light availability, and enrichment of longer wavelengths than are typically usable for oxygenic photosynthesis. Some cyanobacteria from the genus Chroococcidiopsis can use this light to photosynthesize, in a process known as far-red light photoacclimation, or FaRLiP. This genus has commonly been reported from both hot and cold deserts. However, not all Chroococcidiopsis strains carry FaRLiP genes, thus motivating our study into the interplay between FaRLiP and extreme lithic environments. The abundance of sequence data and strains provided the necessary material for an in-depth phylogenetic study, involving spectroscopy, microscopy, and determination of pigment composition, as well as gene and genome analyses. Pigment analyses revealed the presence of red-shifted chlorophylls d and f in all FaRLiP strains tested. In addition, eight genus-level taxa were defined within the encompassing Chroococcidiopsidales, clarifying the phylogeny of this long-standing polyphyletic order. FaRLiP is near universally present in a generalist genus identified in a wide variety of environments, Chroococcidiopsis sensu stricto, while it is rare or absent in closely related, extremophile taxa, including those preferentially inhabiting deserts. This likely reflects the evolutionary process of gene loss in specialist lineages.
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Affiliation(s)
- Laura A Antonaru
- Institute for Experimental Physics, Freie Universität Berlin, Berlin, Germany.
- Department of Life Sciences, Imperial College London, London, UK.
| | - Vera M Selinger
- Institute for Experimental Physics, Freie Universität Berlin, Berlin, Germany
- Dahlem Centre of Plant Sciences, Freie Universität Berlin, Berlin, Germany
| | - Patrick Jung
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Giorgia Di Stefano
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- PhD Program in Cellular and Molecular Biology, Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Nicholas D Sanderson
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Leanne Barker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel J Wilson
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Burkhard Büdel
- Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Daniel P Canniffe
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Daniela Billi
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Dennis J Nürnberg
- Institute for Experimental Physics, Freie Universität Berlin, Berlin, Germany.
- Dahlem Centre of Plant Sciences, Freie Universität Berlin, Berlin, Germany.
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14
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J Ashwini John, Selvarajan E. Genomic analysis of lignocellulolytic enzyme producing novel Streptomyces sp.MS2A for the bioethanol applications. Int J Biol Macromol 2023; 250:126138. [PMID: 37558017 DOI: 10.1016/j.ijbiomac.2023.126138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/22/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023]
Abstract
The conversion of lignocellulosic waste to energy offers a cost-effective biofuel. The current study discusses the utilization of cellulose in rice husks by lichen-associated Streptomyces sp. MS2A via carbohydrate metabolism. Out of 39 actinobacteria, one actinobacterial strain MS2A, showed CMCase, FPase, and cellobiohydrolase activity. The whole genome analysis of Streptomyces sp. MS2A showed maximum similarity with Streptomyces sp. CCM_MD2014. The genome analysis confirmed the presence of cellulose-degrading genes along with xylan-degrading genes that code for GH3, GH6, GH9, GH11, GH43, GH51, and 15 other GH families with glycosyl transferase, carbohydrate-binding modules, and energy metabolism groups. Protein family analysis corroborates the enzyme family. Among the 19,402 genes of Streptomyces sp. MS2A, approximately 70 GH family codes for lignocellulose degradation enzymes. The structure of cellulase was modeled and validated. Scanning electron microscopy and gas chromatography-mass spectrometry (GCMS) was performed to analyze the lignocellulosic degradation of rice husk and the end product bioethanol.
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Affiliation(s)
- J Ashwini John
- Department of Genetic Engineering, School of Bioengineering, Faculty of Engineering and Technology, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603203, India..
| | - Ethiraj Selvarajan
- Department of Genetic Engineering, School of Bioengineering, Faculty of Engineering and Technology, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603203, India..
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15
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Li S, Lian WH, Han JR, Ali M, Lin ZL, Liu YH, Li L, Zhang DY, Jiang XZ, Li WJ, Dong L. Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis. NPJ Biofilms Microbiomes 2023; 9:67. [PMID: 37736746 PMCID: PMC10516943 DOI: 10.1038/s41522-023-00439-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023] Open
Abstract
Deserts occupy one-third of the Earth's terrestrial surface and represent a potentially significant reservoir of microbial biodiversity, yet the majority of desert microorganisms remain uncharacterized and are seen as "microbial dark matter". Here, we introduce a multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, and shotgun metagenomic sequencing. The results showed that CBM captured a significant amount of taxonomic and functional diversity missed in direct sequencing by increasing the recovery of amplicon sequence variants (ASVs) and high/medium-quality metagenome-assembled genomes (MAGs). Importantly, CBM allowed the post hoc recovery of microbes of interest (e.g., novel or specific taxa), even those with extremely low abundance in the culture. Furthermore, strain-level analyses based on CBM and direct sequencing revealed that the desert soils harbored a considerable number of novel bacterial candidates (1941, 51.4%), of which 1095 (from CBM) were culturable. However, CBM would not exactly reflect the relative abundance of true microbial composition and functional pathways in the in situ environment, and its use coupled with direct metagenomic sequencing could provide greater insight into desert microbiomes. Overall, this study exemplifies the CBM strategy with high-resolution is an ideal way to deeply explore the untapped novel bacterial resources in desert soils, and substantially expands our knowledge on the microbial dark matter hidden in the vast expanse of deserts.
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Affiliation(s)
- Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
- School of Life Science, Jiaying University, Meizhou, 514015, China
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Jia-Rui Han
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Mukhtiar Ali
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Zhi-Liang Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Dong-Ya Zhang
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd., Guangzhou, 510700, China
| | - Xian-Zhi Jiang
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd., Guangzhou, 510700, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China.
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16
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Demergasso C, Neilson JW, Tebes-Cayo C, Véliz R, Ayma D, Laubitz D, Barberán A, Chong-Díaz G, Maier RM. Hyperarid soil microbial community response to simulated rainfall. Front Microbiol 2023; 14:1202266. [PMID: 37779711 PMCID: PMC10537920 DOI: 10.3389/fmicb.2023.1202266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/31/2023] [Indexed: 10/03/2023] Open
Abstract
The exceptionally long and protracted aridity in the Atacama Desert (AD), Chile, provides an extreme, terrestrial ecosystem that is ideal for studying microbial community dynamics under hyperarid conditions. Our aim was to characterize the temporal response of hyperarid soil AD microbial communities to ex situ simulated rainfall (5% g water/g dry soil for 4 weeks) without nutrient amendment. We conducted replicated microcosm experiments with surface soils from two previously well-characterized AD hyperarid locations near Yungay at 1242 and 1609 masl (YUN1242 and YUN1609) with distinct microbial community compositions and average soil relative humidity levels of 21 and 17%, respectively. The bacterial and archaeal response to soil wetting was evaluated by 16S rRNA gene qPCR, and amplicon sequencing. Initial YUN1242 bacterial and archaeal 16S rRNA gene copy numbers were significantly higher than for YUN1609. Over the next 4 weeks, qPCR results showed significant increases in viable bacterial abundance, whereas archaeal abundance decreased. Both communities were dominated by 10 prokaryotic phyla (Actinobacteriota, Proteobacteria, Chloroflexota, Gemmatimonadota, Firmicutes, Bacteroidota, Planctomycetota, Nitrospirota, Cyanobacteriota, and Crenarchaeota) but there were significant site differences in the relative abundances of Gemmatimonadota and Chloroflexota, and specific actinobacterial orders. The response to simulated rainfall was distinct for the two communities. The actinobacterial taxa in the YUN1242 community showed rapid changes while the same taxa in the YUN1609 community remained relatively stable until day 30. Analysis of inferred function of the YUN1242 microbiome response implied an increase in the relative abundance of known spore-forming taxa with the capacity for mixotrophy at the expense of more oligotrophic taxa, whereas the YUN1609 community retained a stable profile of oligotrophic, facultative chemolithoautotrophic and mixotrophic taxa. These results indicate that bacterial communities in extreme hyperarid soils have the capacity for growth in response to simulated rainfall; however, historic variations in long-term hyperaridity exposure produce communities with distinct putative metabolic capacities.
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Affiliation(s)
- Cecilia Demergasso
- Biotechnology Center “Profesor Alberto Ruíz”, Universidad Católica del Norte, Antofagasta, Chile
| | - Julia W. Neilson
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Cinthya Tebes-Cayo
- Biotechnology Center “Profesor Alberto Ruíz”, Universidad Católica del Norte, Antofagasta, Chile
- Department of Geology, Faculty of Engineering and Geological Sciences, Universidad Católica del Norte, Antofagasta, Chile
| | - Roberto Véliz
- Biotechnology Center “Profesor Alberto Ruíz”, Universidad Católica del Norte, Antofagasta, Chile
| | - Diego Ayma
- Department of Mathematics, Faculty of Sciences, Universidad Católica del Norte, Antofagasta, Chile
| | - Daniel Laubitz
- Steele Steele Children’s Research Center, Department of Pediatrics, University of Arizona, Tucson, AZ, United States
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Guillermo Chong-Díaz
- Department of Geology, Faculty of Engineering and Geological Sciences, Universidad Católica del Norte, Antofagasta, Chile
| | - Raina M. Maier
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
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17
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Xiao Y, Bao F, Xu X, Yu K, Wu B, Gao Y, Zhang J. The influence of precipitation timing and amount on soil microbial community in a temperate desert ecosystem. Front Microbiol 2023; 14:1249036. [PMID: 37744930 PMCID: PMC10512721 DOI: 10.3389/fmicb.2023.1249036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
Introduction Global climate change may lead to changes in precipitation patterns. This may have a significant impact on the microbial communities present in the soil. However, the way these communities respond to seasonal variations in precipitation, particularly in the context of increased precipitation amounts, is not yet well understood. Methods To explore this issue, a five-year (2012-2016) field study was conducted at the northeast boundary of the Ulan Buh Desert, examining the effects of increased precipitation during different periods of the growing season on both bacterial and fungal communities. The study included five precipitation pattern treatments: a control group (C), as well as groups receiving 50 and 100% of the local mean annual precipitation amount (145 mm) during either the early growing season (E50 and E100) or the late growing season (L50 and L100). The taxonomic composition of the soil bacterial and fungal communities was analyzed using Illumina sequencing. Results After 5 years, the bacterial community composition had significantly changed in all treatment groups, with soil bacteria proving to be more sensitive to changes in precipitation timing than to increased precipitation amounts within the desert ecosystem. Specifically, the alpha diversity of bacterial communities in the late growing season plots (L50 and L100) decreased significantly, while no significant changes were observed in the early growing season plots (E50 and E100). In contrast, fungal community composition remained relatively stable in response to changes in precipitation patterns. Predictions of bacterial community function suggested that the potential functional taxa in the bacterial community associated with the cycling of carbon and nitrogen were significantly altered in the late growing season (L50 and L100). Discussion These findings emphasize the importance of precipitation timing in regulating microbial communities and ecosystem functions in arid regions experiencing increased precipitation amounts.
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Affiliation(s)
- Yao Xiao
- Key Laboratory of Forest Disaster Warning and Control in Yunnan Province, Faculty of Biodiversity Conservation, Southwest Forestry University, Kunming, China
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Fang Bao
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Xiaotian Xu
- Beijing Academy of Forestry and Pomology Sciences, Beijing, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Bo Wu
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Ying Gao
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
- Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Junzhong Zhang
- Key Laboratory of Forest Disaster Warning and Control in Yunnan Province, Faculty of Biodiversity Conservation, Southwest Forestry University, Kunming, China
- Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
- Key Laboratory of State Forestry and Grassland Administration on Highly-Efficient Utilization of Forestry Biomass Resources in Southwest China, Southwest Forestry University, Kunming, China
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18
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Pan X, Raaijmakers JM, Carrión VJ. Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning. Trends Microbiol 2023; 31:959-971. [PMID: 37173204 DOI: 10.1016/j.tim.2023.03.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 05/15/2023]
Abstract
Bacteroidetes are prevalent in soil ecosystems and are associated with various eukaryotic hosts, including plants, animals, and humans. The ubiquity and diversity of Bacteroidetes exemplify their impressive versatility in niche adaptation and genomic plasticity. Over the past decade, a wealth of knowledge has been obtained on the metabolic functions of clinically relevant Bacteroidetes, but much less attention has been given to Bacteroidetes living in close association with plants. To improve our understanding of the functional roles of Bacteroidetes for plants and other hosts, we review the current knowledge of their taxonomy and ecology, in particular their roles in nutrient cycling and host fitness. We highlight their environmental distribution, stress resilience, genomic diversity, and functional importance in diverse ecosystems, including, but not limited to, plant-associated microbiomes.
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Affiliation(s)
- Xinya Pan
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB, Wageningen, The Netherlands; Institute of Biology, Leiden University, Sylviusweg 72, 2333, BE, Leiden, The Netherlands; Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain; Department of Microbiology and Plant Protection, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Málaga, Spain.
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19
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Li S, Yang S, Wei X, Jiao S, Luo W, Chen W, Wei G. Reduced trace gas oxidizers as a response to organic carbon availability linked to oligotrophs in desert fertile islands. THE ISME JOURNAL 2023; 17:1257-1266. [PMID: 37253970 PMCID: PMC10356767 DOI: 10.1038/s41396-023-01437-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/03/2023] [Accepted: 05/19/2023] [Indexed: 06/01/2023]
Abstract
Atmospheric trace gases, such as H2 and CO, are important energy sources for microbial growth and maintenance in various ecosystems, especially in arid deserts with little organic substrate. Nonetheless, the impact of soil organic C availability on microbial trace gas oxidation and the underlying mechanisms are unclear at the community level. This study investigated the energy and life-history strategies of soil microbiomes along an organic C gradient inside and out of Hedysarum scoparium islands dispersed in the Mu Us Desert, China. Metagenomic analysis showed that with increasing organic C availability from bare areas into "fertile islands", the abundance of trace gas oxidizers (TGOs) decreased, but that of trace gas nonoxidizers (TGNOs) increased. The variation in their abundance was more related to labile/soluble organic C levels than to stable/insoluble organic C levels. The consumption rates of H2 and CO confirmed that organic C addition, especially soluble organic C addition, inhibited microbial trace gas oxidation. Moreover, microorganisms with distinct energy-acquiring strategies showed different life-history traits. The TGOs had lower 16 S rRNA operon copy numbers, lower predicted maximum growth rates and higher proportions of labile C degradation genes, implying the prevalence of oligotrophs. In contrast, copiotrophs were prevalent in the TGNOs. These results revealed a mechanism for the microbial community to adapt to the highly heterogeneous distribution of C resources by adjusting the abundances of taxa with distinct energy and life-history strategies, which would further affect trace gas consumption and C turnover in desert ecosystems.
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Affiliation(s)
- Shuyue Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shanshan Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaomeng Wei
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Wen Luo
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
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20
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Grishkan I, Kidron GJ, Rodriguez-Berbel N, Miralles I, Ortega R. Altitudinal Gradient and Soil Depth as Sources of Variations in Fungal Communities Revealed by Culture-Dependent and Culture-Independent Methods in the Negev Desert, Israel. Microorganisms 2023; 11:1761. [PMID: 37512933 PMCID: PMC10383159 DOI: 10.3390/microorganisms11071761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
We examined fungal communities in soil profiles of 0-10 cm depth along the altitudinal gradient of 250-530-990 m.a.s.l. at the Central Negev Desert, Israel, which benefit from similar annual precipitation (95 mm). In the soil samples collected in the summer of 2020, a mycobiota accounting for 169 species was revealed by both culture-dependent and culture-independent (DNA-based) methodologies. The impact of soil depth on the variations in fungal communities was stronger than the impact of altitude. Both methodologies displayed a similar tendency in the composition of fungal communities: the prevalence of melanin-containing species with many-celled large spores (mainly Alternaria spp.) in the uppermost layers and the depth-wise increase in the proportion of light-colored species producing a high amount of small one-celled spores. The culturable and the DNA-based fungal communities had only 13 species in common. The differences were attributed to the pros and cons of each method. Nevertheless, despite the drawbacks, the employment of both methodologies has an advantage in providing a more comprehensive picture of fungal diversity in soils.
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Affiliation(s)
- Isabella Grishkan
- Institute of Evolution, University of Haifa, 199 Aba Khoushy Ave, Mount Carmel, Haifa 3498838, Israel
| | - Giora J Kidron
- Institute of Earth Sciences, The Hebrew University of Jerusalem, Givat Ram Campus, Jerusalem 91904, Israel
| | - Natalia Rodriguez-Berbel
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agrifood, University of Almeria, E-04120 Almería, Spain
| | - Isabel Miralles
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agrifood, University of Almeria, E-04120 Almería, Spain
| | - Raúl Ortega
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agrifood, University of Almeria, E-04120 Almería, Spain
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Chen X, Wang Y, Wang Y, Zhang Y, Shen Y, He X, Xiao C. A Natural Moisture Gradient Affects Soil Fungal Communities on the South Shore of Hulun Lake, Inner Mongolia, China. J Fungi (Basel) 2023; 9:jof9050549. [PMID: 37233260 DOI: 10.3390/jof9050549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/14/2023] [Accepted: 04/30/2023] [Indexed: 05/27/2023] Open
Abstract
Soil moisture content (SWC) can change the diversity and composition of soil fungal communities by affecting soil texture and soil nutrients. To explore the response of soil fungal communities to moisture in the grassland ecosystem on the south shore of Hulun Lake, we set up a natural moisture gradient that was subdivided into high (HW), medium (MW), and low (LW) water contents. Vegetation was investigated by quadrat method, and aboveground biomass was collected by the mowing method. Soil physicochemical properties were obtained by internal experiments. The composition of the soil fungal community was determined using high-throughput sequencing technology. The results showed significant differences in soil texture, nutrients, and fungal species diversity under the moisture gradients. Although there was significant clustering of fungal communities in different treatments, the fungal community composition was not significantly different. According to the phylogenetic tree, the Ascomycota and Basidiomycota were the most important branches. The fungal species diversity was smaller when SWC was higher, and in this environment (HW), the fungal-dominant species were significantly related to SWC and soil nutrients. At this time, soil clay formed a protective barrier for the survival of the dominant classes Sordariomycetes and Dothideomycetes and increased their relative abundance. In summary, the fungal community responded significantly to SWC on the southern shore of the Hulun Lake ecosystem in Inner Mongolia, China, and the fungal community composition of the HW group was stable and easier to survive.
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Affiliation(s)
- Xin Chen
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yujue Wang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yao Wang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yushu Zhang
- Beijing Key Laboratory of Ecological Function Assessment and Regulation Technology of Green Space, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Yuting Shen
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Xiaojia He
- The Administrative Center for China's Agenda 21, Beijing 100038, China
| | - Chunwang Xiao
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
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Liu B, WeiXie L, Deng R, Lei N, Pu S, Li J. Effects of different fertilization methods on Lolium multiflorum Lam. growth and bacterial community in waste slag. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:60538-60551. [PMID: 37036646 DOI: 10.1007/s11356-023-26386-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/07/2023] [Indexed: 04/11/2023]
Abstract
Waste slag has low nutrient content, so it has insufficient nutrient cycling and transformation in the soil ecosystem. There are few studies on the application of oligotrophic phosphate-solubilizing bacteria and phosphate (P) fertilizer to improve the properties of waste slags. In this study, three oligotrophic bacterial strains with P solubilizing activity, namely, Bacillus subtilis 2C (7.23 μg/mL), Bacillus subtilis 6C (4.07 μg/mL), and Bacillus safensis 2N (5.05 μg/mL), were isolated from waste slags. In the pot experiment, compared with no application of P fertilizer, inoculation of Bacillus subtilis 2C with a 50% recommended dose of P fertilizer significantly increased the available phosphorus (AP), total phosphorus (TP), and total nitrogen (TN) in slag by 33.16%, 76.70%, and 233.33%, respectively. The N, P uptake and fresh weight of Lolium multiflorum Lam. were significantly improved by 114.15%, 139.02%, and 100%, respectively. The analysis of the bacterial community showed that the application of P fertilizer decreased the diversity and richness of the bacterial community, and with the addition of phosphorus fertilizer and Bacillus subtilis 2C, the bacterial community in the slag developed towards eutrophication. Redundancy analysis (RDA) showed that the TP content in the slag was significantly correlated with the bacterial community (P = 0.001, < 0.01), followed by the TN content. This study on different P fertilizer application methods can provide some basic ideas for improving the performance of waste slag.
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Affiliation(s)
- Boyu Liu
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, People's Republic of China
| | - LuYao WeiXie
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, People's Republic of China
| | - Ran Deng
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, People's Republic of China
| | - Ningfei Lei
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, People's Republic of China
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution, Chengdu University of Technology, Chengdu, 610059, People's Republic of China
| | - Shengyan Pu
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, People's Republic of China
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution, Chengdu University of Technology, Chengdu, 610059, People's Republic of China
| | - Jing Li
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, 610059, People's Republic of China.
- State Environmental Protection Key Laboratory of Synergetic Control and Joint Remediation for Soil & Water Pollution, Chengdu University of Technology, Chengdu, 610059, People's Republic of China.
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23
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Chen W, Yu T, Zhao C, Li B, Qin Y, Li H, Tang H, Liu J, Zhang X. Development and Determinants of Topsoil Bacterial and Fungal Communities of Afforestation by Aerial Sowing in Tengger Desert, China. J Fungi (Basel) 2023; 9:jof9040399. [PMID: 37108854 PMCID: PMC10144444 DOI: 10.3390/jof9040399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/20/2023] [Accepted: 03/23/2023] [Indexed: 04/29/2023] Open
Abstract
It was previously reported that afforestation in the desert can help improve soil texture, carbon accumulation, and nutrient status. However, the effects of afforestation on soil microbial composition, diversity, and microbial interactions with soil physicochemical properties have been rarely evaluated quantitatively. Using the method of space-for-time substitutions, we assessed the development and determinants of topsoil bacterial and fungal communities over nearly 40 years of successive afforestation by aerial sowing in Tengger Desert, China. The results showed that afforestation by aerial sowing comprised a considerable proportion of Chloroflexi and Acidobacteria in the bacterial community in addition to the ubiquitous phyla found in desert but had fewer effects on the dominant phyla of the fungal community. At the phylum level, the bacterial community was clearly clustered into two groups. However, it was difficult to differentiate the constituents of the fungal community based on principal coordinate analysis. The richness of the bacterial and fungal communities was significantly higher after five years than at zero years and three years. Additionally, the bacterial community varied parabolically and reached its largest size at twenty years, while the fungal community increased exponentially. Soil physicochemical properties were found to have divergent effects on the abundance and diversity of bacterial and fungal communities, among which salt- and carbon-associated properties (e.g., electrical conductivity, calcium, magnesium, total carbon, and organic carbon) were closely related with the abundance of bacterial-dominant phyla and the diversity of bacteria and fungi, but nutrient-associated properties (e.g., total phosphorus and available phosphorus) were not. The results indicate that afforestation through the salt secretions of plants leaves and carbon inputs from litter promote the development of topsoil bacterial and fungal communities in the desert.
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Affiliation(s)
- Weiyu Chen
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Alxa Desert Eco-Hydrology Experimental Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tengfei Yu
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Alxa Desert Eco-Hydrology Experimental Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Chenguang Zhao
- Alxa Institute of Forestry and Grassland, Alxa 750306, China
| | - Baofeng Li
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Alxa Desert Eco-Hydrology Experimental Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yanyan Qin
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Huiying Li
- Alxa Institute of Forestry and Grassland, Alxa 750306, China
| | - Haojie Tang
- Alxa Forestry and Grassland Projection Station, Alxa 750306, China
| | - Junliang Liu
- Alxa Forestry and Grassland Projection Station, Alxa 750306, China
| | - Xiaoyou Zhang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
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Skariah S, Abdul-Majid S, Hay AG, Acharya A, Kano N, Al-Ishaq RK, de Figueiredo P, Han A, Guzman A, Dargham SR, Sameer S, Kim GE, Khan S, Pillai P, Sultan AA. Soil Properties Correlate with Microbial Community Structure in Qatari Arid Soils. Microbiol Spectr 2023; 11:e0346222. [PMID: 36847511 PMCID: PMC10100838 DOI: 10.1128/spectrum.03462-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/05/2023] [Indexed: 03/01/2023] Open
Abstract
This is the first detailed characterization of the microbiota and chemistry of different arid habitats from the State of Qatar. Analysis of bacterial 16S rRNA gene sequences showed that in aggregate, the dominant microbial phyla were Actinobacteria (32.3%), Proteobacteria (24.8%), Firmicutes (20.7%), Bacteroidetes (6.3%), and Chloroflexi (3.6%), though individual soils varied widely in the relative abundances of these and other phyla. Alpha diversity measured using feature richness (operational taxonomic units [OTUs]), Shannon's entropy, and Faith's phylogenetic diversity (PD) varied significantly between habitats (P = 0.016, P = 0.016, and P = 0.015, respectively). Sand, clay, and silt were significantly correlated with microbial diversity. Highly significant negative correlations were also seen at the class level between both classes Actinobacteria and Thermoleophilia (phylum Actinobacteria) and total sodium (R = -0.82 and P = 0.001 and R = -0.86, P = 0.000, respectively) and slowly available sodium (R = -0.81 and P = 0.001 and R = -0.8 and P = 0.002, respectively). Additionally, class Actinobacteria also showed significant negative correlation with sodium/calcium ratio (R = -0.81 and P = 0.001). More work is needed to understand if there is a causal relationship between these soil chemical parameters and the relative abundances of these bacteria. IMPORTANCE Soil microbes perform a multitude of essential biological functions, including organic matter decomposition, nutrient cycling, and soil structure preservation. Qatar is one of the most hostile and fragile arid environments on earth and is expected to face a disproportionate impact of climate change in the coming years. Thus, it is critical to establish a baseline understanding of microbial community composition and to assess how soil edaphic factors correlate with microbial community composition in this region. Although some previous studies have quantified culturable microbes in specific Qatari habitats, this approach has serious limitations, as in environmental samples, approximately only 0.5% of cells are culturable. Hence, this method vastly underestimates natural diversity within these habitats. Our study is the first to systematically characterize the chemistry and total microbiota associated with different habitats present in the State of Qatar.
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Affiliation(s)
- Sini Skariah
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Sara Abdul-Majid
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Anthony G. Hay
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Anushree Acharya
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Noora Kano
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Raghad Khalid Al-Ishaq
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Paul de Figueiredo
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, Bryan, Texas, USA
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - Arum Han
- Department of Electrical and Computer Engineering, Texas A&M University, Texas, USA
- Department of Biomedical Engineering, Texas A&M University, Texas, USA
| | - Adrian Guzman
- Department of Electrical and Computer Engineering, Texas A&M University, Texas, USA
- Department of Biomedical Engineering, Texas A&M University, Texas, USA
| | - Soha Roger Dargham
- Biostatistics, Epidemiology, & Biomathematics Research Core, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Saad Sameer
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Gi Eun Kim
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Sabiha Khan
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Priyamvada Pillai
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
| | - Ali A. Sultan
- Department of Microbiology and Immunology, Weill Cornell Medicine—Qatar, Cornell University, Qatar Foundation—Education City, Doha, Qatar
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25
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Selmani Z, Attard E, Lauga B, Barakat M, Ortet P, Tulumello J, Achouak W, Kaci Y, Heulin T. Culturing the desert microbiota. Front Microbiol 2023; 14:1098150. [PMID: 37113232 PMCID: PMC10126307 DOI: 10.3389/fmicb.2023.1098150] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Over the last 30 years, the description of microbial diversity has been mainly based on culture-independent approaches (metabarcoding and metagenomics) allowing an in-depth analysis of microbial diversity that no other approach allows. Bearing in mind that culture-dependent approaches cannot replace culture-independent approaches, we have improved an original method for isolating strains consisting of "culturing" grains of sand directly on Petri dishes (grain-by-grain method). This method allowed to cultivate up to 10% of the bacteria counted on the surface of grains of the three sites studied in the Great Western Erg in Algeria (Timoudi, Béni Abbès, and Taghit), knowing that on average about 10 bacterial cells colonize each grain. The diversity of culturable bacteria (collection of 290 strains) predicted by 16S rRNA gene sequencing revealed that Arthrobacter subterraneus, Arthrobacter tecti, Pseudarthrobacter phenanthrenivorans, Pseudarthrobacter psychrotolerans, and Massilia agri are the dominant species. The comparison of the culture-dependent and -independent (16S rRNA gene metabarcoding) approaches at the Timoudi site revealed 18 bacterial genera common to both approaches with a relative overestimation of the genera Arthrobacter/Pseudarthrobacter and Kocuria, and a relative underestimation of the genera Blastococcus and Domibacillus by the bacterial culturing approach. The bacterial isolates will allow further study on the mechanisms of tolerance to desiccation, especially in Pseudomonadota (Proteobacteria).
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Affiliation(s)
- Zakia Selmani
- Laboratoire de Biologie et Physiologie des Organismes, Faculté des Sciences Biologiques, University of Science and Technology Houari Boumediene (USTHB), Algiers, Algeria
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Eleonore Attard
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l’Adour, Pau, France
| | - Béatrice Lauga
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l’Adour, Pau, France
| | - Mohamed Barakat
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Philippe Ortet
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Joris Tulumello
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Wafa Achouak
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
| | - Yahia Kaci
- Laboratoire de Biologie et Physiologie des Organismes, Faculté des Sciences Biologiques, University of Science and Technology Houari Boumediene (USTHB), Algiers, Algeria
| | - Thierry Heulin
- CEA, CNRS, BIAM, LEMiRE, Aix-Marseille Université, Saint-Paul-lèz-Durance, France
- *Correspondence: Thierry Heulin,
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Genomic analysis of Paenibacillus sp. MDMC362 from the Merzouga desert leads to the identification of a potentially thermostable catalase. Antonie Van Leeuwenhoek 2023; 116:21-38. [PMID: 36383330 DOI: 10.1007/s10482-022-01793-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 11/01/2022] [Indexed: 11/17/2022]
Abstract
Microorganisms in hot deserts face heat and other environmental conditions, such as desiccation, UV radiation, or low nutrient availability. Therefore, this hostile environment harbour microorganisms with acquired characteristics related to survival in their habitat, which can be exploited in biotechnology. In this work, the genome of Paenibacillus sp. MDMC362 isolated from the Merzouga desert in Morocco was sequenced to understand its survival strategy's genetic basis; and to evaluate the thermostability of a catalase extracted from genomic annotation files using molecular dynamics. Paenibacillus sp. MDMC362 genome was rich in genetic elements involved in the fight against different stresses, notably temperature stress, UV radiations, osmotic stress, carbon starvation, and oxidative stress. Indeed, we could identify genes of the operons groES-groEL and hrcA-grpE-dnaK and those involved in the different stages of sporulation, which can help the bacteria to survive the high temperatures imposed by a desertic environment. We also observed the genetic components of the UvrABC system and additional mechanisms involved in DNA repair, which help overcome UV radiation damage. Other genes have been identified in the genome, like those coding for ectoine and proline, that aids fight osmotic stress and desiccation. Catalase thermostability investigation using molecular dynamics showed that the protein reached stability and conserved its compactness at temperatures up to 373.15 K. These results suggest a potential thermostability of the enzyme. Since the studied protein is a core protein, thermostability could be conserved among Paenibacillus sp. MDMC362 closely related strains; however, bacteria from harsh environments may have a slight advantage regarding protein stability.
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Zhang Z, Chai X, Gao Y, Zhang B, Lu Y, Du Y, Zhang Y, Ding Y, Tariq A, Ullah A, Li X, Zeng F. Alhagi sparsifolia Harbors a Different Root-Associated Mycobiome during Different Development Stages. Microorganisms 2022; 10:microorganisms10122376. [PMID: 36557629 PMCID: PMC9785364 DOI: 10.3390/microorganisms10122376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/22/2022] [Accepted: 11/26/2022] [Indexed: 12/04/2022] Open
Abstract
The mycobiome in the rhizosphere and within the roots benefits the nutrition and function of host plants. However, compared with the bacterial community, root-associated mycobiomes of desert plants and the forces that drive their assemblage are limited. Here, we investigated the mycobiomes in bulk soil, rhizosphere, and root compartments of Alhagi sparsifolia Shap., a phreatophyte species dominating in Central Asia. The internal transcribed spacer (ITS) gene phylogenetic profiles displayed significantly diverse mycobiomes across three compartments and host growth times, together explaining 31.45% of the variation in the community composition. The community structure of the perennial stage was markedly different from that of other stages (30 days to 2 years old). Along the soil-plant continuum, the α-diversity (estimated by Chao1) decreased gradually, while concomitantly increasing the community dissimilarity and the influence of edaphic factors. Specific leaf area, soil water content, and soil organic matter levels were common factors driving the composition of the three mycobiome communities. A more complex and connected network was observed in the root community compared with the other compartments. Overall, our work suggests that an age-sensitive host effect restructured the desert-plant-root-associated mycobiome, and that edaphic factors and host growth strategy may play potential roles in this process.
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Affiliation(s)
- Zhihao Zhang
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- Correspondence: (Z.Z.); (F.Z.)
| | - Xutian Chai
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanju Gao
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Zhang
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
| | - Yan Lu
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
| | - Yi Du
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yulin Zhang
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- College of Resource and Environment Sciences, Xinjiang University, Urumqi 830046, China
| | - Ya Ding
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- College of Resource and Environment Sciences, Xinjiang University, Urumqi 830046, China
| | - Akash Tariq
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
| | - Abd Ullah
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangyi Li
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanjiang Zeng
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Z.Z.); (F.Z.)
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Chilton AM, Nguyen STT, Nelson TM, Pearson LA, Neilan BA. Climate dictates microbial community composition and diversity in Australian biological soil crusts (biocrusts). Environ Microbiol 2022; 24:5467-5482. [PMID: 35769014 PMCID: PMC9796556 DOI: 10.1111/1462-2920.16098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/07/2022] [Indexed: 01/01/2023]
Abstract
The soil surface of drylands can typically be colonized by cyanobacteria and other microbes, forming biological soil crusts or 'biocrusts'. Biocrusts provide critical benefits to ecosystems and are a common component of the largely arid and semi-arid Australian continent. Yet, their distribution and the parameters that shape their microbial composition have not been investigated. We present here the first detailed description of Australia's biocrust microbiome assessed from 15 sites across the continent using 16S rRNA sequencing. The most abundant bacterial phyla from all sites were Cyanobacteria, Proteobacteria, Actinobacteria, Chloroflexi and Bacteroidetes. Cyanobacterial communities from northern regions were more diverse and unclassified cyanobacteria were a noticeable feature of northern biocrusts. Segregation between northern and southern regions was largely due to the differential abundance of Microcoleus spp., with M. paludosus dominating in the north and M. vaginatus dominating in the south. The geographical shifts in bacterial composition and diversity were correlated to seasonal temperatures and summer rainfall. Our findings provide an initial reference for sampling strategies to maximize access to bacterial genetic diversity. As hubs for essential ecosystem services, further investigation into biocrusts in arid and semi-arid regions may yield discoveries of genetic mechanisms that combat increases in warming due to climate change.
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Affiliation(s)
- Angela M. Chilton
- School of Biotechnology and Biomolecular SciencesUniversity of New South WalesNew South WalesAustralia
| | - Suong T. T. Nguyen
- School of Environmental and Life SciencesUniversity of NewcastleCallaghanNew South WalesAustralia
| | - Tiffanie M. Nelson
- School of Environmental and Life SciencesUniversity of NewcastleCallaghanNew South WalesAustralia
| | - Leanne A. Pearson
- School of Environmental and Life SciencesUniversity of NewcastleCallaghanNew South WalesAustralia
| | - Brett A. Neilan
- School of Environmental and Life SciencesUniversity of NewcastleCallaghanNew South WalesAustralia
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29
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Procter M, Kundu B, Sudalaimuthuasari N, AlMaskari RS, Saeed EE, Hazzouri KM, Amiri KMA. Microbiome of Citrullus colocynthis (L.) Schrad. Reveals a Potential Association with Non-Photosynthetic Cyanobacteria. Microorganisms 2022; 10:microorganisms10102083. [PMID: 36296358 PMCID: PMC9607294 DOI: 10.3390/microorganisms10102083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/13/2022] [Accepted: 10/18/2022] [Indexed: 01/24/2023] Open
Abstract
Citrullus colocynthis grows in the sandy desert soil of the Arabian Peninsula with limited access to water, aside from occasional precipitation or dew. Understanding its ability to produce water-filled fruit and nutrient-rich seeds despite the harsh environment, can be useful for agricultural applications. However, information regarding the microbiome of C. colocynthis is lacking. We hypothesized that C. colocynthis associates with bacteria that aid its survival, like what has been observed in other desert plants. Here, we used 16S rRNA gene data to gain insight into the microbiome of C. colocynthis to identify its associated bacteria. In total, 9818 and 6983 OTUs were generated from root, soil, and leaf samples combined. Overall, bulk soils had the highest alpha diversity, followed by rhizosphere and root zone soils. Furthermore, C. colocynthis is associated with known plant-growth-promoting bacteria (including Acidobacteria, Bacterioidetes, and Actinobacteria), and interestingly a class of non-photosynthetic Cyanobacteria (Melainabacteria) that is more abundant on the inside and outside of the root surface than control samples, suggesting its involvement in the rhizophagy process. This study will provide a foundation for functional studies to further understand how C. colocynthis-microbes interactions help them grow in the desert, paving the path for possible agricultural applications.
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Affiliation(s)
- Miranda Procter
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
| | - Biduth Kundu
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
| | - Naganeeswaran Sudalaimuthuasari
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
| | - Raja S. AlMaskari
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
| | - Esam E. Saeed
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
| | - Khaled M. Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
- Correspondence: (K.M.H.); (K.M.A.A.)
| | - Khaled M. A. Amiri
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates
- Correspondence: (K.M.H.); (K.M.A.A.)
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30
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Wang K, Pan R, Fei H, Tong Q, Han F. Changes in soil prokaryotic communities and nitrogen cycling functions along a groundwater table drawdown gradient in desert wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156868. [PMID: 35752234 DOI: 10.1016/j.scitotenv.2022.156868] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Desert wetlands are evolving into deserts by groundwater table (GWT) drawdown. However, the changes in microbial communities and functions during the GWT drawdown are unclear, which hinders the predictive power of biogeochemical processes across the desertification. Here, 16S rRNA gene sequencing, PICRUSt2 and qPCR were used to investigate soil prokaryotic diversity, composition and nitrogen cycling gene abundance at four vegetation types [flooded swamp (FS), drained swamp (DS), desert grassland (DG), and bare sandy land (BS)] along a GWT decline gradient in the Mu Us Desert, northern China. Results showed that prokaryotic Shannon and Chao1 indexes were significantly reduced at BS than those at FS (p < 0.05). Whereas no significant difference was observed between FS, DS and DG (p > 0.05). Distinct shifts in community composition were found along the GWT decline gradient. The dominant taxa gradually changed from obligate anaerobes and eutrophic microbes to facultative anaerobes, and finally to aerobic, oligotrophic and drought-tolerant microbes. Soil moisture was the most important factor in regulating the communities. In addition, GWT drawdown inhibited the relative abundance of genes involved in nitrogen fixation, assimilatory nitrite reduction, and nitrate oxidation, but enhanced the relative abundance of genes related to denitrification, assimilated nitrate reduction, ammonia oxidation and ammonification. Thus, GWT drawdown inhibits nitrogen input potential and exacerbates nitrogen loss potential. These results help in understanding the succession characteristics of desert wetland desertification.
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Affiliation(s)
- Kun Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province 712100, PR China
| | - Ruopeng Pan
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province 712100, PR China
| | - Hongyan Fei
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province 712100, PR China
| | - Qian Tong
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province 712100, PR China
| | - Fengpeng Han
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province 712100, PR China; Research Center on Soil & Water Conservation, Institute of Soil and Water Conservation, Chinese Academy of Sciences Ministry of Water Resources, Yangling, Shaanxi Province 712100, PR China.
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31
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Wagner R, Montoya L, Gao C, Head JR, Remais J, Taylor JW. The air mycobiome is decoupled from the soil mycobiome in the California San Joaquin Valley. Mol Ecol 2022; 31:4962-4978. [PMID: 35933707 PMCID: PMC9624177 DOI: 10.1111/mec.16640] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 07/21/2022] [Accepted: 08/01/2022] [Indexed: 01/07/2023]
Abstract
Dispersal is a key force in the assembly of fungal communities and the air is the dominant route of dispersal for most fungi. Understanding the dynamics of airborne fungi is important for determining their source and for helping to prevent fungal disease. This understanding is important in the San Joaquin Valley of California, which is home to 4.2 million people and where the airborne fungus Coccidioides is responsible for the most important fungal disease of otherwise healthy humans, coccidioidomycosis. The San Joaquin Valley is the most productive agricultural region in the United States, with the principal crops grown therein susceptible to fungal pathogens. Here, we characterize the fungal community in soil and air on undeveloped and agricultural land in the San Joaquin Valley using metabarcoding of the internal transcribed spacer 2 variable region of fungal rDNA. Using 1,002 individual samples, we report one of the most extensive studies of fungi sampled simultaneously from air and soil using modern sequencing techniques. We find that the air mycobiome in the San Joaquin Valley is distinct from the soil mycobiome, and that the assemblages of airborne fungi from sites as far apart as 160 km are far more similar to one another than to the fungal communities in nearby soils. Additionally, we present evidence that airborne fungi in the San Joaquin Valley are subject to dispersal limitation and cyclical intra-annual patterns of community composition. Our findings are broadly applicable to understanding the dispersal of airborne fungi and the taxonomic structure of airborne fungal assemblages.
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Affiliation(s)
- Robert Wagner
- Department of Plant & Microbial BiologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Liliam Montoya
- Department of Plant & Microbial BiologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Cheng Gao
- Institute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Jennifer R. Head
- Division of EpidemiologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Justin Remais
- Division of Environmental Health SciencesUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - John W. Taylor
- Department of Plant & Microbial BiologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
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32
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Nottingham AT, Scott JJ, Saltonstall K, Broders K, Montero-Sanchez M, Püspök J, Bååth E, Meir P. Microbial diversity declines in warmed tropical soil and respiration rise exceed predictions as communities adapt. Nat Microbiol 2022; 7:1650-1660. [PMID: 36065063 DOI: 10.1038/s41564-022-01200-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 07/12/2022] [Indexed: 01/04/2023]
Abstract
Perturbation of soil microbial communities by rising temperatures could have important consequences for biodiversity and future climate, particularly in tropical forests where high biological diversity coincides with a vast store of soil carbon. We carried out a 2-year in situ soil warming experiment in a tropical forest in Panama and found large changes in the soil microbial community and its growth sensitivity, which did not fully explain observed large increases in CO2 emission. Microbial diversity, especially of bacteria, declined markedly with 3 to 8 °C warming, demonstrating a breakdown in the positive temperature-diversity relationship observed elsewhere. The microbial community composition shifted with warming, with many taxa no longer detected and others enriched, including thermophilic taxa. This community shift resulted in community adaptation of growth to warmer temperatures, which we used to predict changes in soil CO2 emissions. However, the in situ CO2 emissions exceeded our model predictions threefold, potentially driven by abiotic acceleration of enzymatic activity. Our results suggest that warming of tropical forests will have rapid, detrimental consequences both for soil microbial biodiversity and future climate.
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Affiliation(s)
- Andrew T Nottingham
- School of Geography, University of Leeds, Leeds, UK. .,School of Geosciences, University of Edinburgh, Edinburgh, UK. .,Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama.
| | - Jarrod J Scott
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | | | - Kirk Broders
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama.,Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service USDA, Peoria, IL, USA
| | | | - Johann Püspök
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Erland Bååth
- Section of Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Patrick Meir
- School of Geosciences, University of Edinburgh, Edinburgh, UK.,Research School of Biology, Australian National University, Canberra, Australia
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33
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Patel SN, Sonani RR, Roy D, Singh NK, Subudhi S, Pabbi S, Madamwar D. Exploring the structural aspects and therapeutic perspectives of cyanobacterial phycobiliproteins. 3 Biotech 2022; 12:224. [PMID: 35975025 PMCID: PMC9375810 DOI: 10.1007/s13205-022-03284-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/28/2022] [Indexed: 11/01/2022] Open
Abstract
Phycobiliproteins (PBPs) of cyanobacteria and algae possess unique light harvesting capacity which expand the photosynthetically active region (PAR) and allow them to thrive in extreme niches where higher plants cannot. PBPs of cyanobacteria/algae vary in abundance, types, amino acid composition and in structure as a function of species and the habitat that they grow in. In the present review, the key aspects of structure, stability, and spectral properties of PBPs, and their correlation with ecological niche of cyanobacteria are discussed. Besides their role in light-harvesting, PBPs possess antioxidant, anti-aging, neuroprotective, hepatoprotective and anti-inflammatory properties, which can be used in therapeutics. Recent developments in therapeutic applications of PBPs are reviewed with special focus on 'route of PBPs administration' and 'therapeutic potential of PBP-derived peptide and chromophores'.
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Affiliation(s)
- Stuti N. Patel
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, Anand, Gujarat 388421 India
- Post-Graduate Department of Biosciences, UGC-Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol, Anand, Gujarat 388315 India
- Present Address: Małopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Ravi R. Sonani
- Present Address: Małopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908 USA
| | - Diya Roy
- Centre for Conservation and Utilisation of Blue Green Algae (CCUBGA), Division of Microbiology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Niraj Kumar Singh
- Department of Biotechnology, Shree A. N. Patel PG Institute of Science and Research, Sardar Patel University, Anand, Gujarat 388001 India
- Present Address: Gujarat Biotechnology Research Centre (GBRC), Deaprtment of Science and Technology (DST), Government of Gujarat, Gandhinagar, Gujarat 382011 India
| | - Sanjukta Subudhi
- The Energy and Resources Institute Darbari Seth Block, India Habitat Centre, Lodi Road, New Delhi, 110003 India
| | - Sunil Pabbi
- Centre for Conservation and Utilisation of Blue Green Algae (CCUBGA), Division of Microbiology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Datta Madamwar
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa, Anand, Gujarat 388421 India
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34
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Cowan DA, Lebre PH, Amon C, Becker RW, Boga HI, Boulangé A, Chiyaka TL, Coetzee T, de Jager PC, Dikinya O, Eckardt F, Greve M, Harris MA, Hopkins DW, Houngnandan HB, Houngnandan P, Jordaan K, Kaimoyo E, Kambura AK, Kamgan-Nkuekam G, Makhalanyane TP, Maggs-Kölling G, Marais E, Mondlane H, Nghalipo E, Olivier BW, Ortiz M, Pertierra LR, Ramond JB, Seely M, Sithole-Niang I, Valverde A, Varliero G, Vikram S, Wall DH, Zeze A. Biogeographical survey of soil microbiomes across sub-Saharan Africa: structure, drivers, and predicted climate-driven changes. MICROBIOME 2022; 10:131. [PMID: 35996183 PMCID: PMC9396824 DOI: 10.1186/s40168-022-01297-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/15/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND Top-soil microbiomes make a vital contribution to the Earth's ecology and harbor an extraordinarily high biodiversity. They are also key players in many ecosystem services, particularly in arid regions of the globe such as the African continent. While several recent studies have documented patterns in global soil microbial ecology, these are largely biased towards widely studied regions and rely on models to interpolate the microbial diversity of other regions where there is low data coverage. This is the case for sub-Saharan Africa, where the number of regional microbial studies is very low in comparison to other continents. RESULTS The aim of this study was to conduct an extensive biogeographical survey of sub-Saharan Africa's top-soil microbiomes, with a specific focus on investigating the environmental drivers of microbial ecology across the region. In this study, we sampled 810 sample sites across 9 sub-Saharan African countries and used taxonomic barcoding to profile the microbial ecology of these regions. Our results showed that the sub-Saharan nations included in the study harbor qualitatively distinguishable soil microbiomes. In addition, using soil chemistry and climatic data extracted from the same sites, we demonstrated that the top-soil microbiome is shaped by a broad range of environmental factors, most notably pH, precipitation, and temperature. Through the use of structural equation modeling, we also developed a model to predict how soil microbial biodiversity in sub-Saharan Africa might be affected by future climate change scenarios. This model predicted that the soil microbial biodiversity of countries such as Kenya will be negatively affected by increased temperatures and decreased precipitation, while the fungal biodiversity of Benin will benefit from the increase in annual precipitation. CONCLUSION This study represents the most extensive biogeographical survey of sub-Saharan top-soil microbiomes to date. Importantly, this study has allowed us to identify countries in sub-Saharan Africa that might be particularly vulnerable to losses in soil microbial ecology and productivity due to climate change. Considering the reliance of many economies in the region on rain-fed agriculture, this study provides crucial information to support conservation efforts in the countries that will be most heavily impacted by climate change. Video Abstract.
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Affiliation(s)
- D A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| | - P H Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| | - Cer Amon
- Institut National Polytechnique Houphouet-Boigny, Cote d'Ivoire, Yamoussoukro, South Africa
| | - R W Becker
- Biodiversity Research Centre, Department of Agriculture and Natural Resources Sciences, Namibia University of Science and Technology, Windhoek, Namibia
| | - H I Boga
- Taita Taveta University, Voi, Kenya
| | - A Boulangé
- Centro de Biotecnologia, Universidade Eduardo Mondlane, Maputo, Mozambique
- UMR InterTryp, CIRAD-IRD, 34398, Montpellier, France
| | - T L Chiyaka
- Department of Biotechnology and Biochemistry, University of Zimbabwe, Harare, Zimbabwe
| | - T Coetzee
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - P C de Jager
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - O Dikinya
- Department of Environmental Science, University of Botswana, Gaborone, Botswana
| | - F Eckardt
- Department of Geography, University of Cape Town, Cape Town, South Africa
| | - M Greve
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - M A Harris
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - D W Hopkins
- Scotland's Rural College, Edinburgh, EH9 3JG, UK
| | - H B Houngnandan
- Université Nationale d'Agriculture, Porto-Novo, Benin (Laboratoire de Microbiologie Des Sols Et d'Ecologie Microbienne), Porto-Novo, Benin
| | - P Houngnandan
- Université Nationale d'Agriculture, Porto-Novo, Benin (Laboratoire de Microbiologie Des Sols Et d'Ecologie Microbienne), Porto-Novo, Benin
| | - K Jordaan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Departamento de Genética Molecular Y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - E Kaimoyo
- University of Zambia, Lusaka, Zambia
| | | | - G Kamgan-Nkuekam
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - T P Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - E Marais
- Gobabeb-Namib Research Institute, Walvis Bay, Namibia
| | - H Mondlane
- Centro de Biotecnologia, Universidade Eduardo Mondlane, Maputo, Mozambique
| | - E Nghalipo
- Biodiversity Research Centre, Department of Agriculture and Natural Resources Sciences, Namibia University of Science and Technology, Windhoek, Namibia
| | - B W Olivier
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - M Ortiz
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - L R Pertierra
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - J-B Ramond
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Departamento de Genética Molecular Y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - M Seely
- Gobabeb-Namib Research Institute, Walvis Bay, Namibia
| | - I Sithole-Niang
- Department of Biotechnology and Biochemistry, University of Zimbabwe, Harare, Zimbabwe
| | - A Valverde
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - G Varliero
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - S Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - D H Wall
- Department of Biology, Colorado State University, Fort Collins, USA
| | - A Zeze
- Institut National Polytechnique Houphouet-Boigny, Cote d'Ivoire, Yamoussoukro, South Africa
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The Role of Thermokarst Lake Expansion in Altering the Microbial Community and Methane Cycling in Beiluhe Basin on Tibetan Plateau. Microorganisms 2022; 10:microorganisms10081620. [PMID: 36014037 PMCID: PMC9412574 DOI: 10.3390/microorganisms10081620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 11/16/2022] Open
Abstract
One of the most significant environmental changes across the Tibetan Plateau (TP) is the rapid lake expansion. The expansion of thermokarst lakes affects the global biogeochemical cycles and local climate regulation by rising levels, expanding area, and increasing water volumes. Meanwhile, microbial activity contributes greatly to the biogeochemical cycle of carbon in the thermokarst lakes, including organic matter decomposition, soil formation, and mineralization. However, the impact of lake expansion on distribution patterns of microbial communities and methane cycling, especially those of water and sediment under ice, remain unknown. This hinders our ability to assess the true impact of lake expansion on ecosystem services and our ability to accurately investigate greenhouse gas emissions and consumption in thermokarst lakes. Here, we explored the patterns of microorganisms and methane cycling by investigating sediment and water samples at an oriented direction of expansion occurred from four points under ice of a mature-developed thermokarst lake on TP. In addition, the methane concentration of each water layer was examined. Microbial diversity and network complexity were different in our shallow points (MS, SH) and deep points (CE, SH). There are differences of microbial community composition among four points, resulting in the decreased relative abundances of dominant phyla, such as Firmicutes in sediment, Proteobacteria in water, Thermoplasmatota in sediment and water, and increased relative abundance of Actinobacteriota with MS and SH points. Microbial community composition involved in methane cycling also shifted, such as increases in USCγ, Methylomonas, and Methylobacter, with higher relative abundance consistent with low dissolved methane concentration in MS and SH points. There was a strong correlation between changes in microbiota characteristics and changes in water and sediment environmental factors. Together, these results show that lake expansion has an important impact on microbial diversity and methane cycling.
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Soil substrate culturing approaches recover diverse members of Actinomycetota from desert soils of Herring Island, East Antarctica. Extremophiles 2022; 26:24. [PMID: 35829965 PMCID: PMC9279279 DOI: 10.1007/s00792-022-01271-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 06/06/2022] [Indexed: 11/12/2022]
Abstract
Antimicrobial resistance is an escalating health crisis requiring urgent action. Most antimicrobials are natural products (NPs) sourced from Actinomycetota, particularly the Streptomyces. Underexplored and extreme environments are predicted to harbour novel microorganisms with the capacity to synthesise unique metabolites. Herring Island is a barren and rocky cold desert in East Antarctica, remote from anthropogenic impact. We aimed to recover rare and cold-adapted NP-producing bacteria, by employing two culturing methods which mimic the natural environment: direct soil culturing and the soil substrate membrane system. First, we analysed 16S rRNA gene amplicon sequencing data from 18 Herring Island soils and selected the soil sample with the highest Actinomycetota relative abundance (78%) for culturing experiments. We isolated 166 strains across three phyla, including novel and rare strains, with 94% of strains belonging to the Actinomycetota. These strains encompassed thirty-five ‘species’ groups, 18 of which were composed of Streptomyces strains. We screened representative strains for genes which encode polyketide synthases and non-ribosomal peptide synthetases, indicating that 69% have the capacity to synthesise polyketide and non-ribosomal peptide NPs. Fourteen Streptomyces strains displayed antimicrobial activity against selected bacterial and yeast pathogens using an in situ assay. Our results confirm that the cold-adapted bacteria of the harsh East Antarctic deserts are worthy targets in the search for bioactive compounds.
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Responses of Cyanobacterial Crusts and Microbial Communities to Extreme Environments of the Stratosphere. Microorganisms 2022; 10:microorganisms10061252. [PMID: 35744770 PMCID: PMC9230428 DOI: 10.3390/microorganisms10061252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/12/2022] [Accepted: 06/17/2022] [Indexed: 12/10/2022] Open
Abstract
How microbial communities respond to extreme conditions in the stratosphere remains unclear. To test this effect, cyanobacterial crusts collected from Tengger Desert were mounted to high balloons and briefly exposed (140 min) to high UV irradiation and low temperature in the stratosphere at an altitude of 32 km. Freezing and thawing treatments were simulated in the laboratory in terms of the temperature fluctuations during flight. Microbial community composition was characterized by sequencing at the level of DNA and RNA. After exposure to the stratosphere, the RNA relative abundances of Kallotenue and Longimicrobium increased by about 2-fold, while those of several dominant cyanobacteria genera changed slightly. The RNA relative abundances of various taxa declined after freezing, but increased after thawing, whereas cyanobacteria exhibited an opposite change trend. The DNA and RNA relative abundances of Nitrososphaeraceae were increased by 1.4~2.3-fold after exposure to the stratosphere or freezing. Exposure to stratospheric environmental conditions had little impact on the total antioxidant capacity, photosynthetic pigment content, and photosynthetic rate, but significantly increased the content of exopolysaccharides by 16%. The three treatments (stratospheric exposure, freezing, and thawing) increased significantly the activities of N-acetyl-β-D-glucosidase (26~30%) and β-glucosidase (14~126%). Our results indicated cyanobacterial crust communities can tolerate exposure to the stratosphere. In the defense process, extracellular organic carbon degradation and transformation play an important role. This study makes the first attempt to explore the response of microbial communities of cyanobacterial crusts to a Mars-like stratospheric extreme environment, which provides a new perspective for studying the space biology of earth communities.
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Vergadi E, Rouva G, Angeli M, Galanakis E. Infectious Diseases Associated with Desert Dust Outbreaks: A Systematic Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19116907. [PMID: 35682493 PMCID: PMC9180817 DOI: 10.3390/ijerph19116907] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 02/04/2023]
Abstract
Background: Desert dust outbreaks and dust storms are the major source of particulate matter globally and pose a major threat to human health. We investigated the microorganisms transported with desert dust particles and evaluated their potential impact on human health. Methods: A systematic review of all reports on the association between non-anthropogenic desert dust pollution, dust microorganisms and human health is conducted. Results: In total, 51 articles were included in this review. The affected regions studied were Asia (32/51, 62.7%) followed by Europe (9/51, 17.6%), America (6/51, 11.8%), Africa (4/51, 7.8%) and Australia (1/51, 2.0%). The Sahara Desert was the most frequent source of dust, followed by Asian and American deserts. In 39/51 studies the dust-related microbiome was analyzed, while, in 12/51 reports, the association of desert dust with infectious disease outbreaks was examined. Pathogenic and opportunistic agents were isolated from dust in 24/39 (61.5%) and 29/39 (74.4%) of the studies, respectively. A significant association of dust events with infectious disease outbreaks was found in 10/12 (83.3%) reports. The infectious diseases that were mostly investigated with dust outbreaks were pneumonia, respiratory tract infections, COVID-19, pulmonary tuberculosis and coccidioidomycosis. Conclusions: Desert dust outbreaks are vehicles of a significant number of pathogenic or opportunistic microorganisms and limited data indicate an association between dust events and infectious disease outbreaks. Further research is required to strengthen the correlation between dust events and infectious diseases and subsequently guide preventive public health measures.
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Marasco R, Fusi M, Ramond JB, Van Goethem MW, Seferji K, Maggs-Kölling G, Cowan DA, Daffonchio D. The plant rhizosheath-root niche is an edaphic "mini-oasis" in hyperarid deserts with enhanced microbial competition. ISME COMMUNICATIONS 2022; 2:47. [PMID: 37938683 PMCID: PMC9723607 DOI: 10.1038/s43705-022-00130-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/04/2022] [Accepted: 05/09/2022] [Indexed: 06/17/2023]
Abstract
Plants have evolved unique morphological and developmental adaptations to cope with the abiotic stresses imposed by (hyper)arid environments. Such adaptations include the formation of rhizosheath-root system in which mutualistic plant-soil microbiome associations are established: the plant provides a nutrient-rich and shielded environment to microorganisms, which in return improve plant-fitness through plant growth promoting services. We hypothesized that the rhizosheath-root systems represent refuge niches and resource islands for the desert edaphic microbial communities. As a corollary, we posited that microorganisms compete intensively to colonize such "oasis" and only those beneficial microorganisms improving host fitness are preferentially selected by plant. Our results show that the belowground rhizosheath-root micro-environment is largely more hospitable than the surrounding gravel plain soil with higher nutrient and humidity contents, and cooler temperatures. By combining metabarcoding and shotgun metagenomics, we demonstrated that edaphic microbial biomass and community stability increased from the non-vegetated soils to the rhizosheath-root system. Concomitantly, non-vegetated soil communities favored autotrophy lifestyle while those associated with the plant niches were mainly heterotrophs and enriched in microbial plant growth promoting capacities. An intense inter-taxon microbial competition is involved in the colonization and homeostasis of the rhizosheath zone, as documented by significant enrichment of antibiotic resistance genes and CRISPR-Cas motifs. Altogether, our results demonstrate that rhizosheath-root systems are "edaphic mini-oases" and microbial diversity hotspots in hyperarid deserts. However, to colonize such refuge niches, the desert soil microorganisms compete intensively and are therefore prepared to outcompete potential rivals.
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Affiliation(s)
- Ramona Marasco
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia.
| | - Marco Fusi
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marc W Van Goethem
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Kholoud Seferji
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | | | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia.
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Gaylarde C, Little B. Biodeterioration of stone and metal - Fundamental microbial cycling processes with spatial and temporal scale differences. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 823:153193. [PMID: 35122860 DOI: 10.1016/j.scitotenv.2022.153193] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Fundamental processes for the biodeterioration of stone and metal involve many of the same microbially mediated reactions - oxidation, reduction, acid dissolution and elemental cycling - resulting from the activities of many of the same groups of environmental microorganisms. Differences depend on the nature of the substratum - stone vs. metal - and the composition of the surroundings, whether terrestrial (stone) or aquatic (stone and metal). Reactions within surface-related biofilms dominate the biodeterioration of metals and contribute greatly to the biodeterioration of stone. In the latter, phototrophic organisms, and especially cyanobacteria, are important first participants, while metal biodeterioration is almost entirely associated with bacteria, archaea and fungi. Biofilms on metal surfaces can produce chemical and electrochemical responses. While electrochemical responses are absent in stone, extracellular electron transfer can be a biodeterioration mechanism in some iron-rich rocks. Microorganisms in biofilms can penetrate and create fissures or cracks in stone and metals. However, the most obvious differences in the reactions of built stone and metal structures are related to the definition of failure, length of time required for a defined failure of the substratum, the area over which the failure occurs and the consequences of failure. Time and space are, similarly, quite distinct for biological breakdown and mineral cycling of metal and stone, with stone/rock cycling potentially occurring over thousands of years and kilometers.
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Affiliation(s)
- Christine Gaylarde
- Department of Microbiology and Plant Biology, Oklahoma University, 770 Van Vleet Oval, Norman, OK 73019, USA
| | - Brenda Little
- BJ Little Corrosion Consulting, LLC, 6528 Alakoko Drive, Diamondhead, MS 39525, USA.
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Liu J, Wang C, Guo Z, Xu A, Pan K, Pan X. The effects of climate on soil microbial diversity shift after intensive agriculture in arid and semiarid regions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153075. [PMID: 35038533 DOI: 10.1016/j.scitotenv.2022.153075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 12/14/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
In arid and semiarid desert areas, climate factors distinctly impact soil microbial community, which can also be greatly altered after agricultural practices at multiple spatial scales. However, it is still poorly unknown whether the effects of climate on soil microbial diversity change after intensive agriculture at a large spatial scale. To uncover this concern, we used time-interval archived soils, taken from paired desert and agricultural experiments at five field stations of the Chinese Ecosystem Research Network across northern China, and performed high-throughput sequencing. Herein, we discovered that the clustering pattern of soil microbial communities was influenced by precipitation at some extent in desert ecosystem, while not impacted by climate factors in agricultural ecosystem. In addition, the analyses on microbial communities presented that the effects of climate factors on the communities decreased after agricultural practices. Soil microbial richness was significantly correlated with environmental temperature in deserts (R = -0.39, P < 0.001) and croplands (R = 0.34, P = 0.004), while the coefficients were opposite; the richness-precipitation relationship was significant in deserts (R = 0.63, P < 0.001) while nonsignificant in croplands (R = -0.03, P = 0.815). Moreover, for the dominant microbial groups (the top 10 phyla), the relationships between their richness and climate factors differed in two land use types, and fewer significant correlations were observed in croplands. In summary, it can be indicated that the influences of climate on soil microbial communities are shifted after intensive agriculture, and the relations of the richness with climate factors are also weakened for both the total and dominant microbial groups. These results improve our comprehension about the effects of climate on soil microbial diversity after intensive agriculture in desert areas, which can help to project microbial diversity in varied land uses under the context of global climate changes.
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Affiliation(s)
- Jie Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Changkun Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiying Guo
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Aiai Xu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Pan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China; National Earth System Science Data Center, Nanjing 210008, China
| | - Xianzhang Pan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Exploring the Diversity and Antibacterial Potentiality of Cultivable Actinobacteria from the Soil of the Saxaul Forest in Southern Gobi Desert in Mongolia. Microorganisms 2022; 10:microorganisms10050989. [PMID: 35630432 PMCID: PMC9147431 DOI: 10.3390/microorganisms10050989] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 12/10/2022] Open
Abstract
Saxaul (Haloxylon ammodendron) is the most widespread plant community in the Gobi Desert in Mongolia, which plays important roles in wind control, sand fixation and water conservation. Investigations of soil-derived actinobacteria inhabiting in the saxaul forest in Gobi Desert in Mongolia have been scarce. In this study, biodiversity of culturable actinobacteria isolated from soil of the saxaul forest in Southern Gobi Aimak (Southern Gobi Province) of Mongolia was characterized and their potential to produce compounds with antibacterial activities was assessed. A total of 172 actinobacterial strains were recovered by culture-based approaches and were phylogenetically affiliated into 22 genera in 13 families of seven orders. Forty-nine actinobacterial isolates were selected to evaluate the antibacterial activities and their underlying mechanism of action was screened by means of a dual-fluorescent reporter assay (pDualrep2). Twenty-three isolates exhibited antagonistic activity against at least one of the tested pathogens, of which two Streptomyces strains can attenuate protein translation by ribosome stalling. Combinational strategies based on modern metabolomics, including bioassay-guided thin-layer chromatography (TLC), UPLC-QTOF-MS/MS based structural annotation and enhanced molecular networking successfully annotated chloramphenicol, althiomycin and granaticin and their derivatives as the antibacterial compounds from extracts in three Streptomyces strains, respectively. This work demonstrates that UPLC-MS/MS-based structural identification and enhanced molecular networking are effective strategies to rapidly illuminate the bioactive chemicals in the microbial extracts. Meanwhile, our results show that the saxaul forest in Mongolia Gobi Desert is a prospective source for discovering novel actinobacteria and biologically active compounds.
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Fusi M, Marasco R, Ramond JB, Barausse A, Baldanzi S. Editorial: Fluctuating Habitats: Ecological Relevance of Environmental Variability and Predictability on Species, Communities, and Ecosystems. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.907622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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de Los Ríos A, Garrido-Benavent I, Limón A, Cason ED, Maggs-Kölling G, Cowan D, Valverde A. Novel lichen-dominated hypolithic communities in the Namib Desert. MICROBIAL ECOLOGY 2022; 83:1036-1048. [PMID: 34312709 PMCID: PMC9015988 DOI: 10.1007/s00248-021-01812-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
The ventral surfaces of translucent rocks from hot desert pavements often harbor hypolithic microbial communities, which are mostly dominated by cyanobacteria. The Namib Desert fog belt supports extensive hypolithic colonization of quartz rocks, which are also colonized by lichens on their dorsal surfaces. Here, we aim to evaluate whether lichens colonize the ventral surface of the rocks (i.e., show hypolithic lifestyle) and compare the bacterial composition of these coastal hypolithic communities with those found inland. Fungal DNA barcoding and fungal and bacterial Illumina metabarcoding were combined with electron microscopy to characterize the composition and spatial structure of hypolithic communities from two (coastal and inland) areas in the Namib Desert. We report, for the first time, the structure and composition of lichen-dominated hypolithic communities found in the coastal zone of the Namib Desert with extensive epilithic lichen cover. Lichen modified areoles with inverted morphology of the genus Stellarangia (three lineages) and Buellia (two lineages) were the main components of these hypolithic communities. Some of these lineages were also found in epilithic habitats. These lichen-dominated hypolithic communities differed in structural organization and bacterial community composition from those found in inland areas. The hypolithic lichen colonization characterized here seems not to be an extension of epilithic or biological soil crust lichen growths but the result of specific sublithic microenvironmental conditions. Moisture derived from fog and dew could be the main driver of this unique colonization.
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Affiliation(s)
- Asunción de Los Ríos
- Biogeochemistry and Microbial Ecology Department, Museo Nacional de Ciencias Naturales, CSIC, Serrano 115 dpdo, 28006, Madrid, Spain.
| | - Isaac Garrido-Benavent
- Biogeochemistry and Microbial Ecology Department, Museo Nacional de Ciencias Naturales, CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
- Departament de Botànica i Geologia, Facultat de Ciències Biològiques, Universitat de València (UV), C. Doctor Moliner 50, 46100, Burjassot, València, Spain
| | - Alicia Limón
- Biogeochemistry and Microbial Ecology Department, Museo Nacional de Ciencias Naturales, CSIC, Serrano 115 dpdo, 28006, Madrid, Spain
| | - Errol D Cason
- Department of Animal Science, University of the Free State, Bloemfontein, South Africa
| | | | - Don Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Angel Valverde
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), C/ Cordel de Merinas 40-52, 37008, Salamanca, Spain
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Abstract
Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N2O), a potent greenhouse gas.
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Schiro G, Chen Y, Blankinship JC, Barberán A. Ride the dust: Linking dust dispersal and spatial distribution of microorganisms across an arid landscape. Environ Microbiol 2022; 24:4094-4107. [PMID: 35384241 DOI: 10.1111/1462-2920.15998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 11/30/2022]
Abstract
In arid ecosystems, where the soil is directly exposed to the action of the wind due to sparse vegetation, dust aerosolization is a consequence of soil degradation and concomitantly, a major vector of microbial dispersal. Disturbances such as livestock grazing or fire can exacerbate wind erosion and dust production. Here, we sampled surface soils in 29 locations across an arid landscape in southwestern USA and characterized their prokaryotic and fungal communities. At four of these locations, we also sampled potential fugitive dust. By comparing the composition of soil and dust samples, we determined the role of dust dispersal in structuring the biogeography of soil microorganisms across the landscape. For Bacteria/Archaea, we found dust associated taxa to have on average, higher regional occupancies compared to soil associated taxa. Complementarily, we found dust samples to harbor a higher amount of widely distributed taxa compared to soil samples. Overall, our study shows how dust dispersal plays a role in the spatial distribution of soil Bacteria/Archaea, but not soil Fungi, and might inform indicators of soil health and stability in arid ecosystems. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Gabriele Schiro
- Department of Environmental Science, University of Arizona, Tucson, Arizona, 85721, USA
| | - Yongjian Chen
- Department of Environmental Science, University of Arizona, Tucson, Arizona, 85721, USA
| | - Joseph C Blankinship
- Department of Environmental Science, University of Arizona, Tucson, Arizona, 85721, USA
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, Arizona, 85721, USA
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Nair A, Ghugare GS, Khairnar K. An Appraisal of Bacteriophage Isolation Techniques from Environment. MICROBIAL ECOLOGY 2022; 83:519-535. [PMID: 34136953 DOI: 10.1007/s00248-021-01782-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/23/2021] [Indexed: 06/12/2023]
Abstract
Researchers have recently renewed interest in bacteriophages. Being valuable models for the study of eukaryotic viruses, and more importantly, natural killers of bacteria, bacteriophages are being tapped for their potential role in multiple applications. Bacteriophages are also being increasingly sought for bacteriophage therapy due to rising antimicrobial resistance among pathogens. Reports show that there is an increasing trend in therapeutic application of natural bacteriophages, genetically engineered bacteriophages, and bacteriophage-encoded products as antimicrobial agents. In view of these applications, the isolation and characterization of bacteriophages from the environment has caught attention. In this review, various methods for isolation of bacteriophages from environmental sources like water, soil, and air are comprehensively described. The review also draws attention towards a handful on-field bacteriophage isolation techniques and the need for their further rapid development.
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Affiliation(s)
- Aparna Nair
- Environmental Virology Cell, Council of Scientific and Industrial Research-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Gaurav S Ghugare
- Environmental Virology Cell, Council of Scientific and Industrial Research-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Krishna Khairnar
- Environmental Virology Cell, Council of Scientific and Industrial Research-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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48
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Shu WS, Huang LN. Microbial diversity in extreme environments. Nat Rev Microbiol 2022; 20:219-235. [PMID: 34754082 DOI: 10.1038/s41579-021-00648-y] [Citation(s) in RCA: 126] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 01/02/2023]
Abstract
A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.
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Affiliation(s)
- Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People's Republic of China.
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
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Naidoo Y, Valverde A, Pierneef RE, Cowan DA. Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils. MICROBIAL ECOLOGY 2022; 83:689-701. [PMID: 34105010 DOI: 10.1007/s00248-021-01785-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/27/2021] [Indexed: 06/12/2023]
Abstract
Precipitation is one of the major constraints influencing the diversity, structure, and activity of soil microbial communities in desert ecosystems. However, the effect of changes in precipitation on soil microbial communities in arid soil microbiomes remains unresolved. In this study, using 16S rRNA gene high-throughput sequencing and shotgun metagenome sequencing, we explored changes in taxonomic composition and functional potential across two zones in the Namib Desert with contrasting precipitation regime. We found that precipitation regime had no effect on taxonomic and functional alpha-diversity, but that microbial community composition and functional potential (beta-diversity) changed with increased precipitation. For instance, Acidobacteriota and 'resistance to antibiotics and toxic compounds' related genes were relatively more abundant in the high-rainfall zone. These changes were largely due to a small set of microbial taxa, some of which were present in low abundance (i.e. members of the rare biosphere). Overall, these results indicate that key climatic factors (i.e. precipitation) shape the taxonomic and functional attributes of the arid soil microbiome. This research provides insight into how changes in precipitation patterns associated with global climate change may impact microbial community structure and function in desert soils.
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Affiliation(s)
- Yashini Naidoo
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa.
| | - Angel Valverde
- IRNASA-CSIC, C/Cordel de Merinas 40-52, 37008, Salamanca, Spain
| | - Rian E Pierneef
- Biotechnology Platform, Agricultural Research Council, Soutpan Road, Onderstepoort Campus, Pretoria, 0110, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
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50
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Wan Y, Zong C, Li X, Wang A, Li Y, Yang T, Bao Q, Dubow M, Yang M, Rodrigo LA, Mao C. New Insights for Biosensing: Lessons from Microbial Defense Systems. Chem Rev 2022; 122:8126-8180. [PMID: 35234463 DOI: 10.1021/acs.chemrev.1c01063] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microorganisms have gained defense systems during the lengthy process of evolution over millions of years. Such defense systems can protect them from being attacked by invading species (e.g., CRISPR-Cas for establishing adaptive immune systems and nanopore-forming toxins as virulence factors) or enable them to adapt to different conditions (e.g., gas vesicles for achieving buoyancy control). These microorganism defense systems (MDS) have inspired the development of biosensors that have received much attention in a wide range of fields including life science research, food safety, and medical diagnosis. This Review comprehensively analyzes biosensing platforms originating from MDS for sensing and imaging biological analytes. We first describe a basic overview of MDS and MDS-inspired biosensing platforms (e.g., CRISPR-Cas systems, nanopore-forming proteins, and gas vesicles), followed by a critical discussion of their functions and properties. We then discuss several transduction mechanisms (optical, acoustic, magnetic, and electrical) involved in MDS-inspired biosensing. We further detail the applications of the MDS-inspired biosensors to detect a variety of analytes (nucleic acids, peptides, proteins, pathogens, cells, small molecules, and metal ions). In the end, we propose the key challenges and future perspectives in seeking new and improved MDS tools that can potentially lead to breakthrough discoveries in developing a new generation of biosensors with a combination of low cost; high sensitivity, accuracy, and precision; and fast detection. Overall, this Review gives a historical review of MDS, elucidates the principles of emulating MDS to develop biosensors, and analyzes the recent advancements, current challenges, and future trends in this field. It provides a unique critical analysis of emulating MDS to develop robust biosensors and discusses the design of such biosensors using elements found in MDS, showing that emulating MDS is a promising approach to conceptually advancing the design of biosensors.
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Affiliation(s)
- Yi Wan
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Chengli Zong
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Xiangpeng Li
- Department of Bioengineering and Therapeutic Sciences, Schools of Medicine and Pharmacy, University of California, San Francisco, 1700 Fourth Street, Byers Hall 303C, San Francisco, California 94158, United States
| | - Aimin Wang
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Yan Li
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Tao Yang
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Qing Bao
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Michael Dubow
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198 CNRS, CEA, Université Paris-Saclay, Campus C.N.R.S, Bâtiment 12, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Mingying Yang
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Ledesma-Amaro Rodrigo
- Imperial College Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States.,School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
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